JPRED-2 Add alscript to the Git repository
[jpred.git] / sources / alscript / doc / alscript.ps
diff --git a/sources/alscript/doc/alscript.ps b/sources/alscript/doc/alscript.ps
new file mode 100644 (file)
index 0000000..43ff0f2
--- /dev/null
@@ -0,0 +1,1668 @@
+%!PS-Adobe-2.0
+%%Creator: dvips 5.516 Copyright 1986, 1993 Radical Eye Software
+%%Title: alscript.dvi
+%%CreationDate: Wed Jun  5 17:35:54 1996
+%%Pages: 34
+%%PageOrder: Ascend
+%%BoundingBox: 0 0 596 842
+%%DocumentFonts: Times-Bold Times-Italic Times-Roman Courier
+%%EndComments
+%DVIPSCommandLine: dvips alscript -o
+%DVIPSSource:  TeX output 1996.06.05:1642
+%%BeginProcSet: tex.pro
+/TeXDict 250 dict def TeXDict begin /N{def}def /B{bind def}N /S{exch}N
+/X{S N}B /TR{translate}N /isls false N /vsize 11 72 mul N /hsize 8.5 72
+mul N /landplus90{false}def /@rigin{isls{[0 landplus90{1 -1}{-1 1}
+ifelse 0 0 0]concat}if 72 Resolution div 72 VResolution div neg scale
+isls{landplus90{VResolution 72 div vsize mul 0 exch}{Resolution -72 div
+hsize mul 0}ifelse TR}if Resolution VResolution vsize -72 div 1 add mul
+TR matrix currentmatrix dup dup 4 get round 4 exch put dup dup 5 get
+round 5 exch put setmatrix}N /@landscape{/isls true N}B /@manualfeed{
+statusdict /manualfeed true put}B /@copies{/#copies X}B /FMat[1 0 0 -1 0
+0]N /FBB[0 0 0 0]N /nn 0 N /IE 0 N /ctr 0 N /df-tail{/nn 8 dict N nn
+begin /FontType 3 N /FontMatrix fntrx N /FontBBox FBB N string /base X
+array /BitMaps X /BuildChar{CharBuilder}N /Encoding IE N end dup{/foo
+setfont}2 array copy cvx N load 0 nn put /ctr 0 N[}B /df{/sf 1 N /fntrx
+FMat N df-tail}B /dfs{div /sf X /fntrx[sf 0 0 sf neg 0 0]N df-tail}B /E{
+pop nn dup definefont setfont}B /ch-width{ch-data dup length 5 sub get}
+B /ch-height{ch-data dup length 4 sub get}B /ch-xoff{128 ch-data dup
+length 3 sub get sub}B /ch-yoff{ch-data dup length 2 sub get 127 sub}B
+/ch-dx{ch-data dup length 1 sub get}B /ch-image{ch-data dup type
+/stringtype ne{ctr get /ctr ctr 1 add N}if}B /id 0 N /rw 0 N /rc 0 N /gp
+0 N /cp 0 N /G 0 N /sf 0 N /CharBuilder{save 3 1 roll S dup /base get 2
+index get S /BitMaps get S get /ch-data X pop /ctr 0 N ch-dx 0 ch-xoff
+ch-yoff ch-height sub ch-xoff ch-width add ch-yoff setcachedevice
+ch-width ch-height true[1 0 0 -1 -.1 ch-xoff sub ch-yoff .1 add]{
+ch-image}imagemask restore}B /D{/cc X dup type /stringtype ne{]}if nn
+/base get cc ctr put nn /BitMaps get S ctr S sf 1 ne{dup dup length 1
+sub dup 2 index S get sf div put}if put /ctr ctr 1 add N}B /I{cc 1 add D
+}B /bop{userdict /bop-hook known{bop-hook}if /SI save N @rigin 0 0
+moveto /V matrix currentmatrix dup 1 get dup mul exch 0 get dup mul add
+.99 lt{/QV}{/RV}ifelse load def pop pop}N /eop{SI restore showpage
+userdict /eop-hook known{eop-hook}if}N /@start{userdict /start-hook
+known{start-hook}if pop /VResolution X /Resolution X 1000 div /DVImag X
+/IE 256 array N 0 1 255{IE S 1 string dup 0 3 index put cvn put}for
+65781.76 div /vsize X 65781.76 div /hsize X}N /p{show}N /RMat[1 0 0 -1 0
+0]N /BDot 260 string N /rulex 0 N /ruley 0 N /v{/ruley X /rulex X V}B /V
+{}B /RV statusdict begin /product where{pop product dup length 7 ge{0 7
+getinterval dup(Display)eq exch 0 4 getinterval(NeXT)eq or}{pop false}
+ifelse}{false}ifelse end{{gsave TR -.1 -.1 TR 1 1 scale rulex ruley
+false RMat{BDot}imagemask grestore}}{{gsave TR -.1 -.1 TR rulex ruley
+scale 1 1 false RMat{BDot}imagemask grestore}}ifelse B /QV{gsave
+transform round exch round exch itransform moveto rulex 0 rlineto 0
+ruley neg rlineto rulex neg 0 rlineto fill grestore}B /a{moveto}B /delta
+0 N /tail{dup /delta X 0 rmoveto}B /M{S p delta add tail}B /b{S p tail}
+B /c{-4 M}B /d{-3 M}B /e{-2 M}B /f{-1 M}B /g{0 M}B /h{1 M}B /i{2 M}B /j{
+3 M}B /k{4 M}B /w{0 rmoveto}B /l{p -4 w}B /m{p -3 w}B /n{p -2 w}B /o{p
+-1 w}B /q{p 1 w}B /r{p 2 w}B /s{p 3 w}B /t{p 4 w}B /x{0 S rmoveto}B /y{
+3 2 roll p a}B /bos{/SS save N}B /eos{SS restore}B end
+%%EndProcSet
+%%BeginProcSet: texps.pro
+TeXDict begin /rf{findfont dup length 1 add dict begin{1 index /FID ne 2
+index /UniqueID ne and{def}{pop pop}ifelse}forall[1 index 0 6 -1 roll
+exec 0 exch 5 -1 roll VResolution Resolution div mul neg 0 0]/Metrics
+exch def dict begin Encoding{exch dup type /integertype ne{pop pop 1 sub
+dup 0 le{pop}{[}ifelse}{FontMatrix 0 get div Metrics 0 get div def}
+ifelse}forall Metrics /Metrics currentdict end def[2 index currentdict
+end definefont 3 -1 roll makefont /setfont load]cvx def}def
+/ObliqueSlant{dup sin S cos div neg}B /SlantFont{4 index mul add}def
+/ExtendFont{3 -1 roll mul exch}def /ReEncodeFont{/Encoding exch def}def
+end
+%%EndProcSet
+TeXDict begin 39158280 55380996 1000 300 300
+(/tmp_mnt/home/weevil/gjb/c/alscript.2.03/doc/alscript.dvi)
+@start /Fa 190[29 65[{}1 39.999962 /Times-Roman rf /Fb
+81[33 52[30 30 43 30 33 20 23 27 1[33 30 33 50 17 33
+1[17 33 30 20 27 33 27 1[30 8[43 60 43 43 40 33 43 1[37
+47 43 56 40 47 1[23 47 1[37 40 43 43 40 43 7[30 30 30
+30 30 30 30 30 30 30 17 15 20 15 10[20 33[{}59 59.999973
+/Times-Bold rf /Fc 134[22 22 33 22 25 14 19 19 1[25 25
+25 36 14 22 1[14 25 25 14 22 25 22 25 25 9[41 30 1[28
+25 30 1[30 1[33 41 28 2[17 1[36 3[33 1[30 6[17 7[25 1[25
+1[12 17 5[17 5[17 33[{}43 50.000000 /Times-Italic rf
+/Fd 133[30 30 30 30 30 30 30 30 30 30 30 30 30 30 30
+30 1[30 30 30 30 30 30 30 30 30 1[30 2[30 1[30 1[30 30
+30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30
+30 30 30 30 2[30 30 30 1[30 30 30 30 30 30 30 30 30 30
+30 1[30 30 30 1[30 30 30 4[30 30 34[{}74 50.000000 /Courier
+rf /Fe 3 63 df<70F8F8F87005057C840E>58 D<0000001800000078000001E0000007
+8000001E00000078000003E000000F8000003C000000F0000003C000000F0000003C0000
+00F0000000F00000003C0000000F00000003C0000000F00000003C0000000F80000003E0
+000000780000001E0000000780000001E000000078000000181D1C7C9926>60
+D<C0000000F00000003C0000000F00000003C0000000F00000003E0000000F80000001E0
+000000780000001E0000000780000001E00000007800000078000001E00000078000001E
+00000078000001E000000F8000003E000000F0000003C000000F0000003C000000F00000
+00C00000001D1C7C9926>62 D E /Ff 134[25 25 36 25 28 17
+19 22 1[28 25 28 41 14 2[14 28 25 17 22 28 22 28 25 10[36
+36 33 28 36 39 30 39 36 47 33 39 1[19 39 1[30 33 36 36
+33 36 7[25 25 25 25 25 25 25 25 25 25 1[12 17 45[{}54
+50.000000 /Times-Bold rf /Fg 134[36 1[52 36 40 24 28
+32 1[40 36 40 60 20 2[20 40 36 24 32 40 32 40 36 10[52
+52 48 40 52 1[44 56 52 68 48 56 1[28 56 1[44 48 52 52
+48 52 7[36 36 36 36 36 36 36 36 36 36 1[18 24 45[{}52
+72.000000 /Times-Bold rf /Fh 69[22 10[28 28 3[22 45[10
+1[22 25 25 36 25 25 14 19 17 25 25 25 25 39 14 25 14
+14 25 25 17 22 25 22 25 22 6[30 36 36 47 36 36 30 28
+33 36 28 36 36 44 30 36 19 17 36 36 28 30 36 33 33 36
+46 1[28 28 28 1[14 25 25 25 25 25 25 25 25 25 25 14 12
+17 12 28 25 17 17 17 39 41 1[25 20 17 33[{}86 50.000000
+/Times-Roman rf /Fi 134[30 30 1[30 30 17 23 20 1[30 30
+30 1[17 30 1[17 30 30 20 27 30 27 30 27 8[43 2[43 1[33
+40 43 33 43 1[53 37 43 8[40 14[30 1[30 2[15 46[{}35 59.999973
+/Times-Roman rf /Fj 134[27 4[17 1[23 2[30 30 7[17 27
+3[30 22[27 2[43 4[37 19[15 46[{}12 59.999973 /Times-Italic
+rf /Fk 138[57 34 40 46 57 57 52 57 86 29 2[29 1[52 1[46
+57 46 1[52 10[75 75 69 57 75 1[63 3[69 2[40 1[80 3[75
+1[75 13[52 52 1[52 1[26 34 45[{}32 103.666679 /Times-Bold
+rf end
+%%EndProlog
+%%BeginSetup
+%%Feature: *Resolution 300dpi
+TeXDict begin
+%%PaperSize: a4
+
+%%EndSetup
+%%Page: 0 1
+0 0 bop 666 338 a Fk(User)26 b(Guide)g(to)173 463 y(ALSCRIPT)f(-)h
+(Sequence)h(alignment)f(to)744 587 y(PostScript)703 712
+y(V)-10 b(ersion)25 b(2.03)751 937 y Fj(Geoffr)n(ey)13
+b(J.)i(Barton)538 1161 y Fi(Laboratory)d(of)j(Molecular)e(Biophysics)
+721 1236 y(University)g(of)i(Oxford)699 1311 y(Rex)g(Richards)e
+(Building)759 1386 y(South)i(Parks)f(Road)756 1460 y(Oxford)h(OX1)g
+(3QU)915 1535 y(U.K.)746 1745 y Fh(T)m(el:)i(\(44\))12
+b(1865-275368)740 1805 y(Fax:)17 b(\(44\))12 b(1865-510454)693
+1866 y(e-mail:)17 b(gjb@bioch.ox.ac.uk)824 2001 y(REFERENCE:)768
+2061 y(Barton,)12 b(G.)h(J.)h(\(1993\),)393 2121 y(ALSCRIPT)f(a)f(tool)
+g(to)g(format)g(multiple)f(sequence)i(alignments)487
+2181 y(Protein)e(Engineering,)i(V)-6 b(olume)11 b(6,)i(No.)18
+b(1,)13 b(pp.37-40.)p eop
+%%Page: 1 2
+1 1 bop 164 316 a Fg(Contents)164 428 y Ff(1)50 b(Update)11
+b(History)1191 b(1)164 538 y(2)50 b(Read)12 b(This)g(First)h(-)f
+(VERSION)h(2.0)844 b(2)164 648 y(3)50 b(Related)11 b(Pr)o(ograms)1136
+b(2)164 758 y(4)50 b(A)l(vailability)1272 b(2)164 868
+y(5)50 b(Installing)11 b(ALSCRIPT)1054 b(2)164 978 y(6)50
+b(Brief)12 b(Description)g(of)g(ALSCRIPT)835 b(3)164
+1088 y(7)50 b(New)12 b(Featur)o(es)h(in)f(V)-5 b(ersion)13
+b(1.4.4)889 b(4)164 1198 y(8)50 b(New)12 b(Featur)o(es)h(in)f(V)-5
+b(ersion)13 b(1.4.5)g(-)f(Pr)o(ogram)i(alsnum)489 b(4)164
+1308 y(9)50 b(New)12 b(Featur)o(es)h(in)f(V)-5 b(ersion)13
+b(2.0)926 b(5)239 1368 y Fh(9.1)52 b(New)13 b(Step)f(1)g(Commands)44
+b Fe(:)24 b(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h
+(:)f(:)h(:)f(:)h(:)f(:)68 b Fh(5)239 1428 y(9.2)52 b(New)13
+b(Step)f(2)g(Commands)44 b Fe(:)24 b(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)
+f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)68 b
+Fh(6)239 1488 y(9.3)52 b(New)13 b(special)g(TEXT)g(commands)18
+b Fe(:)24 b(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f
+(:)h(:)f(:)68 b Fh(7)164 1598 y Ff(10)25 b(Running)11
+b(ALSCRIPT)1070 b(8)239 1659 y Fh(10.1)27 b(Basic)13
+b(Use)46 b Fe(:)25 b(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)
+h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)68
+b Fh(8)239 1719 y(10.2)27 b(More)13 b(complex)f(ef)o(fects)g(-)g(T)m
+(ext)g(Lines,)i(and)e(Masks)50 b Fe(:)25 b(:)f(:)g(:)h(:)f(:)h(:)f(:)h
+(:)f(:)43 b Fh(10)164 1829 y Ff(1)m(1)28 b(Using)12 b(Colour)1210
+b(12)164 1939 y(12)25 b(The)12 b(MASK)g(command)h(family)878
+b(12)239 1999 y Fh(12.1)27 b(Summary)11 b(of)h(mask)h(commands)37
+b Fe(:)24 b(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f
+(:)h(:)f(:)43 b Fh(13)164 2109 y Ff(13)25 b(Printing)11
+b(ALSCRIPT)j(Files)941 b(15)164 2219 y(14)25 b(Conclusion)1255
+b(15)164 2329 y(15)25 b(Appendices)1247 b(15)239 2389
+y Fh(15.1)27 b(ALSCRIPT)13 b(Command)f(Summary)45 b Fe(:)24
+b(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(15)353 2449 y(15.1.1)36 b(STEP)12 b(1)h(COMMANDS)50
+b Fe(:)25 b(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h
+(:)f(:)43 b Fh(16)961 2607 y(1)p eop
+%%Page: 2 3
+2 2 bop 353 315 a Fh(15.1.2)36 b(REQUIRED)13 b(STEP)g(1)f(COMMANDS)17
+b Fe(:)25 b(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(16)353 376 y(15.1.3)36 b(OPTIONAL)12 b(STEP)h(1)f(COMMANDS)20
+b Fe(:)25 b(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(17)353 436 y(15.1.4)36 b(STEP)12 b(2)h(COMMANDS)50
+b Fe(:)25 b(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h
+(:)f(:)43 b Fh(20)239 496 y(15.2)27 b(AMPS)12 b(Block)h(\256le)f
+(format)26 b Fe(:)e(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f
+(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43 b Fh(24)239 556 y(15.3)27
+b(PostScript)12 b(Fonts)33 b Fe(:)24 b(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h
+(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(25)239 616 y(15.4)27 b(386)12 b(DOS)h(installation)k
+Fe(:)24 b(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f
+(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43 b Fh(26)239 677 y(15.5)27
+b(TECHNICAL)14 b(NOTES)22 b Fe(:)j(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h
+(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(27)239 737 y(15.6)27 b(Unix)12 b(Installation)25
+b Fe(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)
+h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43 b Fh(27)239 797
+y(15.7)27 b(V)-6 b(AX/VMS)12 b(Installation)k Fe(:)25
+b(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f
+(:)h(:)f(:)h(:)f(:)43 b Fh(28)239 857 y(15.8)27 b(Alternative)12
+b(ways)h(of)f(invoking)f(ALSCRIPT)32 b Fe(:)24 b(:)h(:)f(:)h(:)f(:)g(:)
+h(:)f(:)h(:)f(:)h(:)f(:)43 b Fh(28)239 917 y(15.9)27
+b(Program)11 b(Crashes)i(and)g(Known)f(Bugs)46 b Fe(:)25
+b(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(29)239 978 y(15.10)r(W)n(ish)13 b(List)g(for)e(next)i(version!!)37
+b Fe(:)24 b(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h
+(:)f(:)h(:)f(:)43 b Fh(30)239 1038 y(15.1)n(1)t(Acknowledgements)g
+Fe(:)24 b(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f
+(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43 b Fh(30)239 1098 y(15.12)r
+(References)25 b Fe(:)g(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f
+(:)h(:)f(:)h(:)f(:)h(:)f(:)h(:)f(:)g(:)h(:)f(:)h(:)f(:)h(:)f(:)43
+b Fh(30)164 1267 y Fg(1)72 b(Update)17 b(History)164
+1439 y Fd(VERSION)29 b(1.0)89 b(19)30 b(June)149 b(1992)164
+1499 y(Version)29 b(1.1)89 b(26)30 b(June)149 b(1992)164
+1559 y(Version)29 b(1.2)89 b(21)30 b(October)59 b(1992:)29
+b(Add)h(multiple)f(blocks)g(per)h(page)f(option.)164
+1620 y(Version)g(1.3)89 b(15)30 b(November)f(1992:)g(First)h
+(Distribution.)164 1680 y(Version)f(1.4)119 b(6)30 b(December)f(1992:)g
+(Add)h(Colour)f(commands.)164 1740 y(Version)g(1.4.1)59
+b(1)30 b(February)f(1993:)g(Small)h(bug)f(fixes)h(-)f(FULL)h(RE-)164
+1800 y(LEASE)f(VERSION.)164 1860 y(Version)g(1.4.2)g(15)h(February)f
+(1993:)g(Make)h(silent_mode)e(toggle.)164 1921 y(Version)h(1.4.3)59
+b(1)30 b(March)119 b(1993:)29 b(Fix)h(bug)f(in)h(colour)f(option.)164
+1981 y(Version)g(1.4.4)g(24)h(March)119 b(1993:)29 b(Add)h(mask)f
+(features)g(\(should)g(be)h(ver-)164 2041 y(sion)f(1.5\).)164
+2101 y(Version)g(1.4.5)g(25)h(May)179 b(1993:)29 b(Include)g(alsnum)h
+(program)f(in)g(distribution.)373 2161 y(7)h(June)149
+b(1993:)29 b(Fix)h(NO_NUMBERS)f(bug)g(in)h(documentation)1120
+2222 y(Change)g(defaults)f(for)g(-q)h(op-)164 2282 y(tion)f(to)h(use)g
+(MASK.)164 2402 y(Version)f(2.0)89 b(23)30 b(May)119
+b(1995:)30 b(Numerous)f(changes)g(and)g(addi-)164 2462
+y(tions)g(including)g(the)961 2607 y Fh(2)p eop
+%%Page: 3 4
+3 3 bop 164 315 a Fd(option)29 b(to)h(colour)f(backgrounds)164
+376 y(differently,)g(ommission)f(of)i(idents)f(on)164
+436 y(second)g(and)h(subsequent)f(lines,)g(helix,)164
+496 y(strand)g(and)h(other)f(special)g(characters,)164
+556 y(relative)g(numbering,)g(error)g(checking)g(of)164
+616 y(ranges)g(on)h(input,)f(bounding)g(box,)164 677
+y(screening,)g(conservation)f(colouring...)164 737 y(Version)h(2.03)89
+b(5)30 b(June)149 b(1996:)29 b(Small)h(bug)f(fixes)h(-)f(patches)g
+(incorporated.)164 797 y(BACKGROUND_REGION)f(and)i(BOUNDING_BOX)e
+(commands)h(moved)g(to)164 857 y(step)g(1)h(section.)164
+1087 y Fg(2)72 b(Read)17 b(This)g(First)h(-)g(VERSION)e(2.0)164
+1198 y Fh(This)d(manual)f(describes)h(an)g(interim)e(release)i(of)f
+(ALSCRIPT)h(that)g(includes)f(many)h(addi-)164 1259 y(tional)c
+(features)g(over)g(the)h(previously)f(distributed)f(V)-6
+b(ersion)10 b(1.4.5.)18 b(I)9 b(had)h(hoped)f(to)g(make)h(a)164
+1319 y(lot)h(more)g(changes)h(and)f(improvements)g(before)g
+(distributing)f(the)h(new)h(version,)f(however)164 1379
+y(I)16 b(have)h(not)g(had)f(the)h(time)f(to)h(do)f(this.)32
+b(I)16 b(am)h(distributing)e(V)-6 b(ersion)17 b(2.0)g(since)g(the)g
+(new)164 1439 y(features)e(have)g(been)h(used)f(in)g(a)h(number)e(of)h
+(published)g(alignment)g(\256gures.)27 b(Please)15 b(see)164
+1499 y(see)e(the)f(Section)g(9)25 b(for)12 b(details)g(of)g(the)g(new)h
+(features.)164 1669 y Fg(3)72 b(Related)17 b(Pr)o(ograms)164
+1780 y Fh(The)12 b(AMPS)g(package)g(\(Barton,)g(1990\).)17
+b(This)c(performs)e(multiple)g(sequence)h(alignments)164
+1840 y(and)g(databank)h(scanning.)164 1901 y(AMAS)h(\(Livingstone)f
+(and)g(Barton,)h(1993,)g(CABIOS,)g(9,)g(745-756\).)21
+b(Analysis)14 b(of)f(Mul-)164 1961 y(tiply)h(Aligned)f(Sequences.)24
+b(This)15 b(package)f(uses)h(a)g(sophisticated)f(set-based)h(method)e
+(to)164 2021 y(identify)e(patterns)i(of)f(residue)g(conservation)g(in)g
+(multiple)g(sequence)h(alignments.)164 2081 y(All)k(programs)f(are)h
+(available)g(by)g(anonymous)f(ftp)h(from)f(geof)o(f.biop.ox.ac.uk.)33
+b(Please)164 2141 y(see)11 b(the)g(README)h(\256le)f(for)f(details)h
+(licencing)f(and)h(registration.)17 b(Y)-5 b(ou)10 b(can)h(read)g
+(manuals)164 2202 y(for)h(the)g(programs)f(and)i(some)f(related)g
+(papers)h(at)f(http://geof)o(f.biop.ox.ac.uk/.)961 2607
+y(3)p eop
+%%Page: 4 5
+4 4 bop 164 315 a Fg(4)72 b(A)-5 b(vailability)164 427
+y Fh(ALSCRIPT)9 b(is)g(available)f(free)g(of)g(char)o(ge)g(for)g
+(academic)h(and)f(non-commercial)f(purposes.)164 487
+y(Distribution)16 b(is)i(by)f(anonymous)g(ftp)f(from)h(geof)o
+(f.biop.ox.ac.uk.)33 b(See)17 b(the)h(README)164 547
+y(\256le)f(on)g(the)g(ftp)f(server)h(for)f(details.)33
+b(Y)-5 b(ou)17 b(need)g(to)g(register)g(with)f(G.)i(J.)g(Barton)f
+(before)164 608 y(downloading)12 b(the)g(software.)164
+777 y Fg(5)72 b(Installing)17 b(ALSCRIPT)164 889 y Fh(See)12
+b(the)h(appropriate)e(section)i(for)e(the)h(computer)g(type)g(you)g
+(are)h(using:)164 949 y(For)g(PCs)i(see)f(see)h(Section)f(15.4.)23
+b(For)14 b(Unix)f(see)i(see)g(Section)e(15.6)i(.)23 b(For)13
+b(VMS)i(see)f(see)164 1009 y(Section)e(15.7)g(.)164 1178
+y Fg(6)72 b(Brief)17 b(Description)f(of)i(ALSCRIPT)164
+1290 y Fh(ALSCRIPT)c(takes)h(a)f(multiple)f(sequence)i(alignment)e(in)h
+(AMPS)g(\(Barton)f(&)h(Sternber)o(g,)164 1350 y(1987,)23
+b(Barton,)f(1990\))e(block-\256le)f(format)h(and)g(a)h(set)g(of)f
+(formatting)f(commands)h(and)164 1410 y(produces)e(a)h(PostScript)f
+(\256le)g(that)g(may)h(be)g(printed)e(on)i(a)g(PostScript)e(laser)i
+(printer)n(,)g(or)164 1470 y(viewed)8 b(using)g(a)g(PostScript)g
+(previewer)g(\(e.g.)16 b(Sun)8 b(Microsystem')m(s)g(PageV)m(iew)g
+(program\).)164 1531 y(CLUST)l(AL)i(and)f(GCG)g(format)e(multiple)h
+(alignment)g(\256les)h(may)f(also)h(be)g(used)g(\(see)g(below\).)164
+1591 y(ALSCRIPT)h(is)h(NOT)g(a)f(multiple)f(sequence)i(alignment)e
+(program,)h(nor)g(is)g(it)g(an)h(alignment)164 1651 y(editor)m(.)164
+1711 y(Given)k(a)g(block-\256le)f(and)h(pointsize)g(\(character)f
+(width/height\),)g(ALSCRIPT)h(calculates)164 1771 y(how)g(many)g
+(residues)h(can)f(be)h(\256tted)f(across)h(the)f(page,)h(and)g(how)f
+(many)g(sequences)h(will)164 1832 y(\256t)d(down)f(the)h(page,)h(it)e
+(then)h(prints)g(the)g(alignment)f(at)h(the)g(chosen)g(pointsize)g(on)g
+(as)g(many)164 1892 y(pages)h(as)g(are)g(needed.)22 b(Running)13
+b(ALSCRIPT)h(with)f(a)h(smaller)f(or)g(lar)o(ger)g(pointsize)g(will)164
+1952 y(automatically)f(re-scale)g(the)h(alignment)f(to)g(\256t)g(on)g
+(fewer)g(or)h(more)e(pages)j(as)f(appropriate.)164 2012
+y(The)i(actual)f(page)h(dimensions)f(may)h(be)f(re-set)g(to)g(any)h
+(value,)g(so)g(if)f(you)g(have)g(access)i(to)164 2072
+y(an)11 b(A3)g(PostScript)f(printer)n(,)h(or)g(typesetting)g(machine,)g
+(alignments)g(can)h(readily)e(be)h(scaled)164 2133 y(to)h(maximise)g
+(the)h(available)f(space.)164 2193 y(Each)j(output)g(page)g(has)g
+(three)g(basic)g(regions.)26 b(The)15 b(left)f(hand)h(edge)g(contains)g
+(identi\256er)164 2253 y(codes)f(for)e(each)i(sequence.)22
+b(The)14 b(main)f(part)g(of)g(the)h(page)f(holds)h(the)f(alignment,)h
+(and)f(the)164 2313 y(top)c(part,)i(the)e(position)g(numbers)h(and)f
+(tick)h(marks.)17 b(ALSCRIPT)10 b(commands)g(make)f(use)h(of)164
+2373 y(a)k(character)g(coordinate)f(system)i(for)e(font)g(changes,)j
+(and)e(other)f(formatting)g(commands.)164 2433 y(Thus,)d(any)f(residue)
+f(in)g(the)g(alignment)g(may)g(be)g(referred)f(to)h(by)g(its)h
+(sequence)g(position)f(num-)961 2607 y(4)p eop
+%%Page: 5 6
+5 5 bop 164 315 a Fh(ber)13 b(\(x-axis\))f(and)h(sequence)h(number)e
+(\(y-axis\),)h(similarly)m(,)g(ranges)g(of)f(residue)i(positions,)164
+376 y(or)e(sequences)h(may)g(also)f(be)h(de\256ned)f(in)g(the)g
+(character)g(coordinate)g(system.)164 436 y(The)h(basic)g(ALSCRIPT)f
+(commands)h(allow)f(the)g(following)f(functionality:)164
+496 y(Fonts:)28 b(Any)18 b(PostScript)f(font)g(at)h(any)g(size)g(may)g
+(be)g(de\256ned)f(and)h(used)g(on)g(individual)164 556
+y(residues,)13 b(regions)f(or)g(identi\256er)f(codes.)164
+616 y(Boxing:)16 b(Simple)8 b(rectangular)h(boxes)g(may)g(be)g(drawn)g
+(around)g(any)g(part)f(of)h(the)g(alignment.)164 677
+y(Particular)i(residue)g(types)h(may)g(be)g(selected)g(and)g
+(automatically)f("surrounded")h(by)f(lines.)164 737 y(For)e(example,)h
+(if)g(the)f(characters)h('G')f(and)g('P')g(are)g(selected,)j(then)d
+(lines)h(will)f(not)h(be)f(drawn)164 797 y(between)i(G)g(and)h(P)f
+(characters,)h(but)e(only)h(where)g(G)h(and)f(P)g(border)f(with)h
+(other)g(characters.)164 857 y(Shading:)24 b(Grey)16
+b(shading)g(of)f(any)h(level)g(from)f(black)g(to)h(white)g(may)g(be)g
+(applied)f(to)h(any)164 917 y(region)k(of)h(the)g(alignment,)i(either)d
+(as)i(a)f(rectangular)g(region,)i(or)d(as)i(residue)f(speci\256c)164
+978 y(shading.)d(e.g.)h("shade)13 b(all)g(Cys)g(residues)f(between)h
+(positions)f(6)h(and)f(30")164 1038 y(T)m(ext:)23 b(Speci\256c)14
+b(text)h(strings)g(may)g(be)g(added)g(to)g(the)g(alignment)f(at)h(any)g
+(position)g(and)g(in)164 1098 y(any)d(font)g(or)g(font)g(size.)164
+1158 y(Lines:)22 b(Horizontal)13 b(or)h(vertical)g(lines)g(may)g(be)g
+(drawn)g(to)g(the)g(left,)h(right,)f(top)g(or)g(bottom)164
+1218 y(of)e(any)g(residue)h(position)f(or)g(group)f(of)h(positions.)164
+1279 y(Colour:)17 b(Characters)c(or)f(character)g(backgrounds)g(may)g
+(be)g(independently)g(coloured.)164 1339 y(The)e(example)e(block)h
+(\256le)g("example1.blc")h(and)f(command)g(\256le)f("example1.als")j
+(illustrate)164 1399 y(most)h(of)g(these)h(commands)f(in)h(action.)164
+1459 y(Although)7 b(written)g(with)g(the)g(aim)g(of)g(producing)g
+(\256gures)g(for)g(journal)g(submission,)h(ALSCRIPT)164
+1519 y(may)i(be)h(used)g(as)g(a)f(tool)g(for)g(interpreting)f(multiple)
+g(sequence)j(alignments.)17 b(For)10 b(example,)164 1579
+y(the)h(boxing,)h(shading)g(and)f(font)g(changing)g(facilities)h(can)f
+(be)h(applied)f(to)h(highlight)e(amino)164 1640 y(acids)h(of)f(a)g
+(particular)g(type)g(and)h(thus)f(draw)g(attention)g(to)g(clusters)h
+(of)f(positive)g(or)g(negative)164 1700 y(char)o(ge,)j(hydrophobics,)f
+(etc.)164 1869 y Fg(7)72 b(New)17 b(Featur)o(es)f(in)i(V)-7
+b(ersion)18 b(1.4.4)164 1981 y Fh(This)h(version)e(introduces)h(the)g
+(MASK)g(family)f(of)h(commands)g(which)g(allows)g(boxing,)164
+2041 y(shading)11 b(etc)h(to)f(be)h(applied)f(according)g(to)g(the)h
+(frequency)e(of)i(occurence)f(of)g(the)g(character)164
+2101 y(types)f(at)g(each)g(position)g(in)f(the)h(alignment.)17
+b(For)9 b(example,)i(it)e(is)h(possible)h(to)e(box)h(positions)164
+2161 y(where)i(one)f(character)h(is)g(seen)g(in)g(more)f(than)h(N)f(of)
+h(the)f(sequences.)20 b(It)11 b(is)h(also)g(possible)g(to)164
+2222 y(box/shade)d(etc)g(the)f(most)h(frequently)e(occurring)h
+(character)g(at)h(each)g(position.)17 b(Commands)164
+2282 y(exist)c(to)g(select)h(which)f(characters)g(will)g(be)g(used)h
+(in)f(the)g(calculation)f(of)h(frequencies)g(and)164
+2342 y(which)k(will)g(be)h(excluded,)h(thus)e(boxing)g(can)h(be)f
+(based)h(upon)f(two)h(or)f(more)f(character)164 2402
+y(types)c(at)g(a)g(position.)17 b(MASK)12 b(commands)g(also)g(exist)g
+(to)f(show)h(residues)g(identical)f(to)h(one)164 2462
+y(sequence)h(in)f(the)h(set.)18 b(See)13 b(the)f(section)h(on)f(MASK)g
+(below)g(for)g(details.)961 2607 y(5)p eop
+%%Page: 6 7
+6 6 bop 164 315 a Fh(NOTE:)20 b(Although)f(boxing)g(according)g(to)g
+(the)h(frequency)f(of)g(amino)g(acids)h(seen)g(at)g(a)164
+376 y(position)8 b(is)g(a)g(popular)g(method)g(of)g(representation)g
+(it)g(is)g(not)g(usually)g(the)g(most)g(informative.)164
+436 y(An)13 b(analysis)i(that)e(takes)h(into)f(account)h(the)f
+(physico-chemical)g(properties)g(of)g(the)g(amino)164
+496 y(acids)g(and)f(also)h(relates)f(the)h(amino)f(acid)g(similarities)
+g(to)g(the)h(overall)e(similarity)h(between)164 556 y(the)h(sequences)g
+(is)g(more)g(helpful)f(in)g(identifying)g(functionally)f(important)h
+(residues.)19 b(The)164 616 y(AMAS)f(program)g(\(Livingstone)g(and)g
+(Barton,)i(1993\))e(applies)g(a)h(\257exible)f(hierarchical)164
+677 y(set-based)13 b(approach)f(to)g(this)g(problem.)164
+846 y Fg(8)72 b(New)17 b(Featur)o(es)f(in)i(V)-7 b(ersion)18
+b(1.4.5)f(-)h(Pr)o(ogram)e(alsnum)164 958 y Fh(V)-6 b(ersion)19
+b(1.4.5)h(includes)f(the)f(program)g("alsnum".)38 b(This)20
+b(is)f(a)g(temporary)f(solution)g(to)164 1018 y(the)e(residue)f
+(numbering)g(problem.)28 b(Ultimately)m(,)16 b(these)g(functions)g
+(will)f(be)h(included)f(as)164 1078 y(alscript)d(commands.)164
+1138 y(alsnum)g(creates)h(a)f(set)h(of)f(TEXT)i(commands)e(that)g(can)g
+(be)h(incorporated)e(into)h(an)g(alscript)164 1198 y(command)i(\256le)g
+(to)g(place)h(sequential)g(numbers)f(at)g(any)h(position)f(in)g(the)g
+(alignment.)24 b(The)164 1259 y(numbers)14 b(ignore)g(gaps,)i(so)f(the)
+g(numbering)e(will)h(correspond)g(to)h(the)f(speci\256c)h(sequence)164
+1319 y(position)d(rather)g(than)g(the)g(alignment.)164
+1379 y(T)m(o)g(use)h(the)f(program:)164 1439 y(1.)31
+b(Decide)17 b(where)f(you)g(want)h(the)f(numbers)g(to)h(be)g(placed.)31
+b(For)15 b(example,)j(you)f(might)164 1499 y(want)12
+b(the)g(numbers)g(above)g(the)g(third)g(sequence)h(in)f(the)g
+(alignment.)17 b(If)12 b(so,)h(make)f(an)g(extra)164
+1559 y(sequence)h(space)g(above)f(the)h(third)e(sequence)i(using)g(the)
+f(ADD)p 1293 1559 15 2 v 18 w(SEQ)g(command.)164 1620
+y(2.)18 b(Decide)13 b(what)f(is)h(the)f(number)f(of)h(the)g(\256rst)g
+(residue)h(of)f(the)g(sequence)h(to)f(be)g(numbered.)164
+1680 y(This)h(will)f(not)g(always)h(be)f(1)h(since)g(you)f(may)g(be)g
+(aligning)g(fragments)g(or)g(domains.)164 1740 y(3.)18
+b(Decide)13 b(the)f(numbering)f(interval)h(\(e.g.)19
+b(every)12 b(10th)g(amino)g(acid\).)164 1800 y(4.)18
+b(Run)13 b(the)f(program.)164 1860 y(For)f(example,)h(if)g(you)f(want)h
+(to)g(add)g(numbers)f(according)g(to)h(sequence)g(37)g(of)g(a)g(block)f
+(\256le)164 1921 y(\(junk.blc\),)k(calling)f(the)h(\256rst)f(residue)h
+(of)f(the)h(sequence)g(12,)h(and)e(with)h(an)f(interval)g(of)h(5,)164
+1981 y(and)g(the)f(numbers)g(are)h(to)f(be)h(placed)g(at)f(the)h
+(location)f(of)g(sequence)i(3)e(in)h(the)f(alignment.)164
+2041 y(T)m(ype:)164 2101 y(alsnum)e(37)h(12)f(5)g(3)h
+Fe(<)f Fh(junk.blc)g Fe(>)h Fh(junk.text)164 2161 y(5.)25
+b(Add)15 b(the)f(resulting)g(TEXT)i(commands)f(from)e(junk.text)i(to)f
+(your)g(alscript)g(command)164 2222 y(\256le.)961 2607
+y(6)p eop
+%%Page: 7 8
+7 7 bop 164 316 a Fg(9)72 b(New)17 b(Featur)o(es)f(in)i(V)-7
+b(ersion)18 b(2.0)164 428 y Fh(Error)9 b(checking)h(is)g(now)g(done)f
+(on)h(all)g(ranges)g(input.)17 b(If)9 b(you)h(run)f(ALSCRIPT)h(2.0)g
+(on)g(a)g(\256le)164 488 y(that)i(worked)f(with)h(ALSCRIPT)g(1.4.5,)h
+(and)f(it)g(complains)f(about)h(out)g(of)f(range)h(numbers,)164
+548 y(then)19 b(check)h(your)f(ranges)h(carefully)m(.)39
+b(If)19 b(you)g(think)g(you)g(are)h(right,)h(then)e(send)h(me)g(a)164
+608 y(minimal)14 b(example)g(of)h(the)f(problem)g(and)h(I)f(will)h
+(investigate.)25 b(V)-6 b(ersions)15 b(of)g(ALSCRIPT)164
+668 y(before)k(2.0)i(would)f(often)f(work)h(happily)f(with)h(out)g(of)g
+(range)g(numbers)f(and)h(produce)164 729 y(perfectly)11
+b(OK)i(output.)164 789 y(The)k(\256les)h Ff(ipns.als)f
+Fh(and)g Ff(ipns.blc)g Fh(show)g(example)g(command)f(and)h(block)g
+(\256le)g(that)f(use)164 849 y(most)c(of)g(these)h(new)g(commands.)18
+b(See)12 b(the)h Fc(examples)f Fh(directory)m(.)164 996
+y Fb(9.1)59 b(New)15 b(Step)g(1)g(Commands)164 1090 y
+Fh(SCREENSIZE)f(120)164 1150 y(Usually)g(you)g(should)g(not)g(need)g
+(to)g(change)g(this)g(value,)h(it)f(alters)g(the)g(screening)g(used)g
+(by)164 1210 y(the)h(printer)m(.)24 b(A)15 b(value)g(of)f(120)h(is)g
+(used)g(by)g(default.)25 b(On)15 b(most)f(300dpi)h(black)f(and)h(white)
+164 1271 y(printers)f(this)h(gives)g(much)f(smoother)g(greys)h(than)f
+(the)h(default)f(used)h(in)g(earlier)f(versions)164 1331
+y(of)e(ALSCRIPT)l(.)164 1391 y(PIR)p 245 1391 15 2 v
+17 w(SA)-6 b(VE)13 b(\256lename)164 1451 y(W)n(ill)h(cause)g(the)g
+(block)g(\256le)g(to)f(be)h(saved)h(into)f(the)f(\256le)h
+(\252\256lename\272)g(in)g(PIR)f(format.)22 b(This)164
+1511 y(can)13 b(be)f(useful)g(for)g(moving)f(block)i(\256le)f
+(alignments)g(to)g(other)g(programs.)164 1572 y(MSF)p
+267 1572 V 18 w(SA)-6 b(VE)12 b(\256lename)164 1632 y(W)n(ill)17
+b(cause)i(the)e(block)h(\256le)f(to)h(be)f(saved)i(into)e(the)g(\256le)
+h(\252\256lename\272)f(in)h(something)f(that)164 1692
+y(approximates)12 b(GCG)g(.msf)h(format.)k Fc(W)-5 b(arning!)19
+b(This)12 b(has)h(not)f(been)g(fully)g(tested.)164 1752
+y Fh(NUMBER)p 379 1752 V 19 w(COLOUR)h(4)164 1812 y(Sets)20
+b(the)g(colour)f(used)h(for)f(numbering)f(at)i(the)g(top)f(of)h(the)f
+(alignment)g(\(no)g(American)164 1872 y(spelling)13 b(at)g(the)g
+(moment\).)19 b(In)13 b(this)g(example,)g(colour)g(number)f(4)h(has)g
+(been)h(de\256ned)e(\(See)164 1933 y(the)g(DEFINE)p 417
+1933 V 18 w(COLOUR)i(command)d(if)h(you)h(are)f(not)g(sure)g(what)h
+(this)f(means\).)164 1993 y(SINGLE)p 344 1993 V 18 w(P)-5
+b(AGE)164 2053 y(If)13 b(this)g(is)h(set,)g(ALSCRIPT)g(assumes)h
+(everything)d(will)h(be)h(plotted)e(on)i(one)f(page.)22
+b(At)13 b(the)164 2113 y(moment,)j(all)g(this)f(does)h(is)g(write)f
+(the)h(bounding)e(box)i(for)e(the)i(\256gure,)g(so)g(encapsulating)164
+2173 y(the)h(PostScript.)31 b(This)18 b Fc(may)f Fh(allow)f(the)h
+(output)g(of)f(alscript)h(to)g(be)g(imported)f(into)h(word)164
+2234 y(processors)c(etc,)g(but)f(probably)f(not)h(all.)164
+2294 y(ID)p 220 2294 V 17 w(ONL)-5 b(Y)p 370 2294 V 19
+w(ON)p 461 2294 V 18 w(FIRST)p 615 2294 V 17 w(LINE)164
+2354 y(If)12 b(this)i(is)f(present,)h(then)f(sequence)g(identi\256ers)g
+(will)f(only)h(be)g(printed)g(on)g(the)g(\256rst)f(line)h(of)164
+2414 y(the)f(alignment.)18 b(Often)12 b(this)g(looks)h(better)f(for)f
+(small)i(alignments)f(than)g(the)g(default.)164 2474
+y(BACKGROUND)p 518 2474 V 18 w(COLOUR)i(7)961 2607 y(7)p
+eop
+%%Page: 8 9
+8 8 bop 164 315 a Fh(Sets)14 b(the)g(colour)f(used)i(for)e(the)h
+(background)f(to)h(the)g(alignment.)23 b(This)15 b(can)f(be)g(useful)g
+(for)164 376 y(preparing)c(\256gures)h(for)g(projection.)17
+b(At)11 b(the)g(moment)g(this)g(only)g(works)g(reliably)g(when)g(the)
+164 436 y(SINGLE)p 344 436 15 2 v 18 w(P)-5 b(AGE)13
+b(is)g(also)f(set.)164 496 y(BOUNDING)p 433 496 V 18
+w(BOX)g(x)g(y)h(x1)f(y1)164 556 y(De\256nes)h(the)g(bounding)f(box)g
+(for)g(the)g(\256gure.)19 b(This)13 b(is)g(set)h(in)e(points)h(\(1/72)f
+(inch\).)18 b(NOTE:)164 616 y(In)12 b(version)g(2.0)h(this)f(was)h(a)g
+(STEP)f(2)h(Command.)164 677 y(BACKGROUND)p 518 677 V
+18 w(REGION)g(x)f(y)h(x1)f(y1)164 737 y(De\256nes)h(the)g(region)f(to)h
+(colour)f(as)i(background)e(-)h(the)f(default)h(is)g(set)g(up)g(for)f
+(A4)h(paper)g(so)164 797 y(US)h(users)h(may)g(have)f(to)h(\256ddle)f
+(with)g(this.)25 b(V)-6 b(alues)15 b(are)g(points)f(\(1/72)g(inch\).)24
+b(NOTE:)15 b(In)164 857 y(version)d(2.0)h(this)f(was)h(a)g(STEP)f(2)h
+(Command.)164 1004 y Fb(9.2)59 b(New)15 b(Step)g(2)g(Commands)164
+1098 y Fh(COLOUR)p 371 1098 V 19 w(TEXT)p 516 1098 V
+19 w(REGION)d(x)h(y)f(x1)g(y1)h(colour)164 1158 y(Sets)8
+b(the)g(colour)g(for)g(TEXT)g(command)g(output.)14 b(Similar)8
+b(syntax)g(to)g(COLOUR)p 1568 1158 V 17 w(REGION,)164
+1218 y(FONT)p 297 1218 V 18 w(REGION)13 b(etc.)164 1279
+y(COLOUR)p 371 1279 V 19 w(LINE)p 503 1279 V 18 w(REGION)g(x)f(y)g(x1)h
+(y1)f(colour)164 1339 y(Set)g(the)g(colour)g(for)g(LINEs)h(in)f(a)h
+(region.)164 1399 y(CALCONS)g(x)f(y)h(x1)f(y1)164 1459
+y(Calculate)21 b(conservation)f(values)h(according)f(to)g(Zvelebil)h
+Fc(et)g(al.)43 b Fh(for)19 b(the)i(designated)164 1519
+y(region.)d(\(See)12 b(Livingstone)g(&)g(Barton)g(1993)g(for)g(details)
+g(and)h(further)e(refs\))164 1579 y(MASK)h(CONSER)l(V)-6
+b(A)g(TION)13 b(cutof)o(f)164 1640 y(If)j(CONSCAL)h(has)g(been)g(used,)
+h(then)f(mask)f(residues)h(according)f(to)h(the)f(conservation)164
+1700 y(cutof)o(f.)164 1760 y(e.g.)28 b(MASK)15 b(CONSER)l(V)-6
+b(A)g(TION)16 b(10)f(would)g(mask)g(all)g(identities,)i(MASK)e(CONSER-)
+164 1820 y(V)-6 b(A)g(TION)14 b(6)h(would)f(mask)h(reasonably)f
+(conserved)g(positions.)25 b(See)14 b(examples)h(for)f(more)164
+1880 y(on)e(this)h(command.)164 1941 y(HELIX)g(x1)f(y)g(x2)164
+2001 y(Draw)g(a)h(helix)f(from)f(x1)h(to)g(x2)h(of)f(sequence)h(y)m(.)
+164 2061 y(STRAND)g(x1)f(y)g(x2)164 2121 y(Draw)g(a)h(strand)f(from)f
+(x1)h(to)h(x2)f(of)g(sequence)h(y)m(.)164 2181 y(COIL)g(x1)f(y)g(x2)164
+2242 y(Draw)g(a)h(coil)f(\(horizontal)f(line\))h(from)f(x1)h(to)g(x2)h
+(of)f(sequence)h(y)m(.)164 2302 y(RELA)-6 b(TIVE)p 403
+2302 V 20 w(T)o(O)13 b(<seqnum>)f(<startnum>)164 2362
+y(Set)20 b(reference)f(numbers)h(to)g(work)f(relative)h(to)g(sequence)g
+(number)g(<seqnum>.)41 b(This)164 2422 y(means)14 b(that)g(in)g(all)f
+(subsequent)i(commands,)f(ALSCRIPT)g(will)g(translate)g(your)f(x)h
+(values)164 2482 y(into)f(absolute)g(position)f(values)i(in)f(the)f
+(alignment.)20 b(This)14 b(is)f Fc(extr)n(emely)h Fh(useful)f(since)g
+(you)961 2607 y(8)p eop
+%%Page: 9 10
+9 9 bop 164 315 a Fh(can)13 b(annotate)g(your)g(alignment)f(using)i
+(your)e(favourite)g(sequences)i(as)g(a)g(reference)e(point.)164
+376 y(Y)-5 b(ou)12 b(no)g(longer)g(have)h(to)f(translate)g(every)g(x)h
+(position)f(into)g(the)g(alignment)g(position.)164 436
+y(<startnum>)c(is)h(optional.)16 b(If)8 b(present,)i(it)e(speci\256es)h
+(what)g(the)f(\256rst)h(residue)f(in)g(the)h(displayed)164
+496 y(sequence)14 b(is.)24 b(For)13 b(example,)h(you)g(may)g(be)g
+(showing)f(residues)h(200-500)f(of)h(a)g(sequence,)164
+556 y(so)f(<startnum>)g(would)f(be)i(200)e(rather)h(than)f(the)h
+(default)g(of)f(1.)20 b Fc(W)-5 b(arning)14 b(-)f(this)g(is)g(a)g(very)
+164 616 y(new)g(featur)n(e)f(and)h(bounds)f(checking)g(is)h(not)f
+(fully)g(enabled)g(for)h(it)p Fh(.)164 677 y(Y)-5 b(ou)8
+b(can)g(use)g(RELA)-6 b(TIVE)p 643 677 15 2 v 20 w(T)o(O)8
+b(several)g(times)g(in)g(the)g(command)g(\256le)g(to)g(annotate)g(dif)o
+(f)o(erent)164 737 y(sequences.)19 b(RELA)-6 b(TIVE)p
+635 737 V 20 w(T)o(O)13 b(0)g(resets)f(to)h(the)f(\252normal\272)g
+(alignment)f(numbering.)164 884 y Fb(9.3)59 b(New)15
+b(special)f(TEXT)h(commands)164 978 y Fh(Some)e(special)i(TEXT)g
+(commands)e(have)h(been)g(added)g(to)g(allow)f(drawing)g(of)h
+(alternative)164 1038 y(shapes)j(etc.)29 b(In)16 b(fact)g(this)g(is)g
+(how)g(the)g(HELIX,)h(STRAND)f(and)g(COIL)g(commands)g(are)164
+1098 y(implemented.)i(The)12 b(text)h(commands)f(are)g(all)g
+(pre\256xed)g(by)g(an)h(@)f(symbol.)164 1158 y(e.g.)19
+b(TEXT)14 b(3)e(6)g(\252@fuparrow\272)164 1218 y(will)g(draw)g(a)h
+(\256lled)e(up)i(arrow)e(at)i(position)f(3,6.)164 1279
+y(The)h(alternative)f(text)g(commands)g(are:)164 1339
+y(@leftarrow)f(-)h(an)g(open)h(left)f(pointing)f(arrow)m(.)164
+1399 y(@\257eftarrow)g(-)h(a)g(\256lled)g(left)g(pointing)g(arrow)m(.)
+164 1459 y(@uparrow)f(-)h(an)h(open)f(up)g(pointing)g(arrow)m(.)164
+1519 y(@fuparrow)f(-)h(a)g(\256lled)g(up)h(pointing)e(arrow)m(.)164
+1580 y(@downarrow)g(-)h(an)h(open)f(down)g(pointing)g(arrow)m(.)164
+1640 y(@fdownarrow)f(-)h(a)g(\256lled)g(down)g(pointing)g(arrow)m(.)164
+1700 y(@circle)g(-)g(an)g(open)h(circle.)164 1760 y(@fcircle)f(-)g(a)g
+(\256lled)g(circle.)164 1820 y(I)g(plan)g(to)g(make)h(this)f(option)g
+(more)g(\257exible)g(in)g(the)g(near)g(future.)164 1990
+y Fg(10)71 b(Running)17 b(ALSCRIPT)164 2116 y Fb(10.1)59
+b(Basic)14 b(Use)164 2210 y Fh(I)h(recommend)g(you)g(read)g(through)g
+(this)g(section,)i(then)e(scan)h(the)g(commands)f(in)g(Section)164
+2270 y(15.1)25 b(to)12 b(get)h(a)f(feel)g(for)g(what)g(ALSCRIPT)h(can)f
+(do.)164 2330 y(See)i(Section)g(15.8for)g(alternative)f(methods)h(of)g
+(invoking)g(ALSCRIPT)l(.)h(In)f(this)g(section,)164 2390
+y(the)9 b(interactive)f(method)h(is)g(described.)17 b(The)10
+b(QUICK)f(ST)l(AR)m(T)h(method)e(shown)i(in)e(Section)961
+2607 y(9)p eop
+%%Page: 10 11
+10 10 bop 164 315 a Fh(15.8)33 b(is)16 b(useful)g(to)g(format)f(a)i
+(sequence)g(alignment)e(quickly)h(using)g(standard)g(pointsize)164
+376 y(and)c(shading.)164 436 y(ALSCRIPT)e(is)f(designed)h(to)f(work)g
+(with)g(AMPS)g(block)g(\256le)g(format)f(multiple)h(alignments.)164
+496 y(If)h(you)h(have)h(a)f(multiple)g(alignment)f(generated)h(by)g
+(CLUST)l(AL)i(V)e(or)g(the)g(GCG)g(package,)164 556 y(then)h(it)g(must)
+h(be)f(translated)g(to)h(AMPS)f(block)g(\256le)g(format.)164
+616 y(T)m(o)18 b(translate)g(a)g(GCG)g(.MSF)g(\256le:)29
+b(T)m(ype:)g(msf2blc.)34 b(T)m(o)18 b(translate)g(a)g(CLUST)l(AL)h(PIR)
+164 677 y(format)11 b(\256le,)i(or)f(any)g(PIR)g(format)f(\256le:)18
+b(clus2blc.)164 737 y(Both)10 b(programs)g(prompt)f(for)g(the)h(name)h
+(of)e(an)i(input)f(\256le,)g(and)h(an)f(output)g(block)g(\256le)g
+(name.)164 797 y(A)i(good)g(convention)g(to)g(follow)g(is)h(to)f(name)g
+(all)h(block\256les)f(with)g(the)g(extension)g(".blc".)164
+857 y(T)m(o)g(run)g(ALSCRIPT)h(simply)f(type:)164 917
+y(alscript)164 978 y(you)f(will)h(then)f(be)h(prompted)f(for)g(the)g
+(name)h(of)f(the)h(ALSCRIPT)g(command)f(\256le.)18 b(Having)164
+1038 y(typed)12 b(the)g(\256lename,)h(the)f(commands)h(will)e(be)i
+(executed)f(as)h(you)g(have)f(speci\256ed.)164 1098 y(A)g(Simple)g
+(Command)g(File)g(\(example.als\))164 1158 y(The)f(\256le)e
+(example.blc)h(contains)h(a)f(small)g(multiple)f(sequence)i(alignment.)
+17 b(The)10 b(following)164 1218 y(ALSCRIPT)k(command)g(\256le)g(will)f
+(convert)h(this)g(into)f(a)h(PostScript)f(alignment)h(\256le)f(in)h(12)
+164 1279 y(point)e(Helvetica.)164 1369 y Fd(#Comments)29
+b(in)h(ALSCRIPT)f(command)g(files)g(start)g(with)h(a)f(#)164
+1429 y(#)164 1489 y(#Commands)g(are)g(free)h(format)f(-)h(separated)f
+(by)g(blank,)h(tab)f(or)h(comma)f(characters)164 1549
+y(#)164 1610 y(BLOCK_FILE)59 b(example.blc)f(#define)29
+b(the)h(block)f(file)h(to)f(format)164 1670 y(OUTPUT_FILE)59
+b(example.ps)28 b(#where)h(to)h(put)g(the)f(result)164
+1730 y(LANDSCAPE)g(#landscape)g(paper)g(orientation)164
+1790 y(POINTSIZE)g(12)h(#12)f(point)g(default)g(pointsize)164
+1850 y(DEFINE_FONT)g(0)g(Helvetica)g(DEFAULT)g(#set)h(font)f(0)h(to)g
+(be)f(Helvetica)164 1911 y(SETUP)g(#Tell)h(the)f(program)g(to)h(get)f
+(on)h(with)g(it.)164 2001 y Fh(Now)21 b(try)g(changing)h(the)f
+(POINTSIZE)h(value)f(to)h(5)f(ALSCRIPT)h(will)f(re-format)f(the)164
+2061 y(alignment)12 b(to)g(make)g(best)h(use)g(of)f(the)g(available)g
+(paper)m(.)164 2121 y(These)g(are)f(all)h(STEP)f(1)h(commands)f(-)g
+(they)g(refer)f(to)h(overall)g(layout,)h(and)f(system)h(settings)164
+2181 y(-)18 b(for)g(example,)i(the)f(paper)f(size)h(or)f(maximum)g
+(sequence)h(length.)37 b(Other)18 b(commonly)164 2242
+y(used)d(STEP)g(1)f(commands)g(are)h(IDENT)p 898 2242
+15 2 v 18 w(WIDTH)f(which)h(reserves)f(more)g(or)g(less)h(width)164
+2302 y(for)d(the)h(sequence)g(identi\256er)f(codes,)i(NUMBER)p
+1051 2302 V 19 w(SEQS)e(which)h(adds)g(a)g(number)f(to)h(each)164
+2362 y(sequence)i(and)f(LINE)p 563 2362 V 19 w(WIDTH)p
+748 2362 V 18 w(F)l(ACT)o(OR)h(which)f(allows)g(the)h(thickness)f(of)g
+(all)h(boxing)164 2422 y(lines)g(to)g(be)h(adjusted.)26
+b(See)15 b(Section)g(15.1)31 b(for)14 b(details)h(of)g(these)h(and)f
+(all)g(other)g(STEP)g(1)164 2482 y(commands.)949 2607
+y(10)p eop
+%%Page: 11 12
+11 11 bop 164 315 a Fh(The)18 b(simple)g(example)g(outlined)f(above)h
+(can)g(be)g(modi\256ed)f(with)g(a)h(variety)f(of)h(STEP)g(2)164
+376 y(commands.)164 436 y(for)12 b(example)g(\256le)g(example2.als:)164
+550 y Fd(#)30 b(FILE)f(example2.als)164 610 y(#)164 670
+y(#Commands)g(are)g(free)h(format)f(-)h(separated)f(by)g(blank,)h(tab)f
+(or)h(comma)f(characters)164 731 y(#)164 791 y(BLOCK_FILE)59
+b(example.blc)f(#define)29 b(the)h(block)f(file)h(to)f(format)164
+851 y(OUTPUT_FILE)59 b(example2.ps)28 b(#where)h(to)h(put)g(the)f
+(result)164 911 y(LANDSCAPE)g(#landscape)g(paper)g(orientation)164
+971 y(POINTSIZE)g(12)h(#12)f(point)g(default)g(pointsize)164
+1032 y(DEFINE_FONT)g(0)g(Helvetica)g(DEFAULT)g(#set)h(font)f(0)h(to)g
+(be)f(Helvetica)164 1092 y(DEFINE_FONT)g(1)g(Helvetica)g(REL)h(0.5)268
+b(#set)30 b(font)f(1)h(to)g(be)f(half)h(sized)f(Helvetica)164
+1152 y(DEFINE_FONT)g(3)g(Helvetica-Bold)g(DEFAULT)118
+b(#set)30 b(font)f(3)h(to)g(be)f(Bold)h(Helvetica)164
+1212 y(DEFINE_FONT)f(4)g(Times-BoldItalic)f(DEFAULT)59
+b(#font)30 b(4)g(is)f(Times-)164 1272 y(BoldItalic)164
+1333 y(NUMBER_SEQS)g(#Number)g(the)g(sequences)g(at)h(left)f(hand)h
+(side)164 1393 y(SETUP)f(#Tell)h(the)f(program)g(to)h(get)f(on)h(with)g
+(it.)164 1453 y(#)164 1513 y(#step)f(2)h(commands)f(come)h(after)f(the)
+g(SETUP)h(command)164 1573 y(#)164 1633 y(#Here)f(are)h(some)f
+(examples...)164 1694 y(#)164 1754 y(SURROUND_CHARS)f(GP)i(ALL)g(#draw)
+f(lines)g(around)g(all)h(G)g(and)f(P)164 1814 y(SHADE_CHARS)g(ILVW)g
+(ALL)h(0.6)f(#shade)g(all)h(I)g(L)f(V)h(and)g(W)g(with)f(value)g(0.6)
+164 1874 y(BOX_REGION)g(1)h(1)f(2)h(20)g(0.8)f(#rectangular)g(box)g
+(from)h(positions)f(1)g(to)h(2)g(of)g(se-)164 1934 y(quences)f(1)h(to)g
+(20)164 1995 y(FONT_CHARS)f(C)h(ALL)f(3)418 b(#Use)30
+b(font)f(3)h(\(BOLD)f(Helvetica\))g(for)h(C)f(characters)164
+2055 y(ID_FONT)g(ALL)h(1)567 b(#set)30 b(identifiers)e(in)i(font)g(1)
+164 2229 y Fh(There)9 b(are)g(many)g(possible)g(ways)g(of)g(combining)f
+(these)h(commands)g(and)g(the)g(others)g(shown)164 2289
+y(in)j(Section)f(15.1)h(.)19 b(In)11 b(general,)h(if)g(you)g(apply)f
+(multiple)h(commands)f(to)h(the)g(same)h(residue,)164
+2350 y(the)j(ef)o(fect)g(of)g(the)g(last)g(applied)g(command)g
+(persists)g(where)g(there)g(would)g(otherwise)g(be)164
+2410 y(a)g(con\257ict.)28 b(Thus)17 b(the)e(intersection)h(of)f(two)h
+(overlapping)e(SHADed)i(regions)f(would)h(be)164 2470
+y(shaded)d(according)g(to)g(the)g(second)g(SHADE)h(command,)f(not)g
+(some)g(mixture)f(of)h(the)g(two.)949 2607 y(1)n(1)p
+eop
+%%Page: 12 13
+12 12 bop 164 315 a Fh(Similarly)9 b(for)g(FONT)h(commands.)18
+b(BOX)10 b(and)g(SURROUND)h(commands)f(behave)g(in)g(the)164
+376 y(opposite)h(sense,)i(all)e(BOXing)g(and)g(SURROUNDing)g(persists)g
+(regardless)h(of)e(how)h(many)164 436 y(commands)k(you)h(issue.)28
+b(This)16 b(makes)f(it)h(possible)f(for)g(example,)h(to)g(SURROUND)f
+(two)164 496 y(dif)o(ferent)c(sets)i(of)f(residues)h(as)g(follows:)164
+648 y Fd(SURROUND_CHARS)28 b(DE)i(ALL)164 708 y(SURROUND_CHARS)e(DEHKR)
+i(ALL)164 860 y Fh(This)13 b(would)g(result)f(in)h(D)f(and)h(E)g
+(characters)g(being)f(partitioned)g(from)f(the)i(rest)g(as)g(well)f(as)
+164 920 y(D)g(E)h(H)g(K)f(R)h(characters)f(\(see)h(Example)f(output\).)
+164 1064 y Fb(10.2)59 b(Mor)o(e)15 b(complex)e(effects)h(-)g(T)-5
+b(ext)14 b(Lines,)h(and)g(Masks)164 1158 y Fh(T)m(ext,)f(lines)g(and)g
+(masking)f(are)h(meant)f(to)g(be)h(used)g(to)f(annotate)h(the)f
+(multiple)g(alignment.)164 1218 y(The)20 b(TEXT)i(command)d(allows)h
+(any)g(piece)g(of)g(text)g(to)g(be)g(located)g(anywhere)f(on)h(the)164
+1279 y(alignment.)33 b(Clearly)m(,)19 b(however)e(it)g(makes)h(little)f
+(sense)i(to)e(superimpose)h(the)f(text)g(over)164 1339
+y(the)c(alignment)e(though)i(this)f(can)h(be)g(done!)18
+b(Accordingly)m(,)12 b(you)g(must)h(\256rst)f(make)g(a)h(space)164
+1399 y(to)i(put)h(the)f(text)g(in.)28 b(Usually)m(,)17
+b(this)e(will)g(be)h(a)g(few)f(lines)h(below)f(the)h(multiple)e
+(sequence)164 1459 y(alignment,)e(but)f(you)h(may)g(want)g(to)f(add)h
+(text)g(at)g(the)g(top,)g(or)g(somewhere)f(in)h(between)g(two)164
+1519 y(sequences.)25 b(Y)-5 b(ou)15 b(can)f(make)h(space)g(in)f(two)g
+(ways.)25 b(Either)14 b(by)h(editing)e(the)i(block-\256le)e(to)164
+1579 y(introduce)f("dummy")g(sequences)i(at)f(the)f(locations)h(you)g
+(want,)g(or)f(by)g(making)h(use)g(of)f(the)164 1640 y(ADD)p
+275 1640 15 2 v 18 w(SEQ)g(command.)164 1700 y(The)h(ADD)p
+365 1700 V 18 w(SEQ)f(command)g(has)h(two)f(ar)o(guments,)h(the)f
+(sequence)h(after)f(which)g(you)g(want)164 1760 y(further)c(sequences)i
+(to)g(be)f(added,)i(and)e(how)g(many)g(blank)h(sequences)g(you)f(need.)
+18 b(Thus,)11 b(we)164 1820 y(can)h(reserve)h(space)g(for)e(5)h(lines)h
+(of)f(text)g(underneath)g(a)g(10)g(sequence)h(multiple)f(alignment)164
+1880 y(with)g(the)g(following)f(command.)164 1941 y(ADD)p
+275 1941 V 18 w(SEQ)h(10)h(5)164 2001 y(we)g(can)f(then)g(put)g(text)h
+(below)f(the)g(alignment)g(at)g(the)h(20th)f(residue.)164
+2061 y(TEXT)i(20)e(13)g("Active)h(Site)f(His")164 2121
+y(or)g(any)g(other)g(position.)164 2181 y(Similarly)m(,)f(we)i(could)f
+(draw)g(a)g(vertical)g(line)g(to)h(point)e(out)i(which)f(residue)g(we)h
+(mean)164 2242 y(LINE)g(LEFT)g(20)g(13)f(1)n(1)164 2302
+y(And)g(change)h(the)f(font)g(of)g(the)g(text)g(to)g(number)g(7)g
+(\(whatever)g(that)g(has)h(been)g(set)f(to\):)164 2362
+y(FONT)p 297 2362 V 18 w(RESIDUE)h(20)f(13)g(7)164 2422
+y(Y)-5 b(ou)16 b(can)h(have)f(multiple)g(ADD)p 751 2422
+V 18 w(SEQ)g(commands,)i(but)e(they)h(must)f(occur)g(in)g(sequence)164
+2482 y(order)m(.)i(Thus:)949 2607 y(12)p eop
+%%Page: 13 14
+13 13 bop 164 315 a Fd(ADD_SEQ)29 b(0)h(5)164 376 y(ADD_SEQ)f(5)h(12)
+164 480 y Fh(is)13 b(legal.)18 b(But)164 575 y Fd(ADD_SEQ)29
+b(5)h(12)164 635 y(ADD_SEQ)f(0)h(5)164 730 y Fh(Is)9
+b(NOT!!)17 b(NO)9 b(CHECKING)h(IS)e(performed)g(by)i(the)f(program)f
+(for)g(this)i(error)e(-)h(so)g(beware!)164 790 y(Note)15
+b(that)g(add)p 441 790 15 2 v 18 w(seq)h(commands)f(refer)f(to)i(the)f
+(actual)g(sequence)h(number)f(as)g(implied)g(by)164 850
+y(the)j(block)f(\256le,)i(not)f(the)g(number)f(after)g(applying)g(the)h
+(add)p 1252 850 V 17 w(seq)h(command.)34 b(Thus,)20 b(for)164
+910 y(a)d(four)e(sequence)j(block)e(\256le,)i(if)e(you)g(want)h(to)f
+(add)h(space)g(for)f(three)g(sequences)i(before)164 970
+y(sequence)13 b(1)f(and)h(two)f(sequences)h(after)f(sequence)h(3,)g
+(the)f(commands)g(would)g(be:)164 1075 y Fd(ADD_SEQ)29
+b(0)h(3)164 1135 y(ADD_SEQ)f(3)h(2)164 1240 y Fh(T)m(ext)13
+b(added)g(with)g(the)g(TEXT)h(command)f(will)g(not)g(be)g(split)g
+(across)h(page)f(breaks,)h(so)f(you)164 1300 y(may)i(in)g(some)h
+(circumstances)g(need)f(to)g(\256ddle)g(a)h(little)f(with)g(the)g
+(location/pointsize)g(for)164 1360 y(the)d(text)g(to)h(get)f(the)g
+(desired)h(result.)164 1420 y(Masking)g(is)g(a)f(technique)h(for)e
+(drawing)h(irregular)f(shaped)i(outlines,)g(or)f(shaded)h(regions)f(-)
+164 1480 y(this)e(should)g(not)g(be)g(confused)g(with)f(the)h(MASK)g
+(family)f(of)h(commands)g(described)g(below)m(.)164 1541
+y(For)18 b(example)h(a)h(histogram)e(can)h(be)h(added)f(to)g(the)g
+(bottom)f(of)h(an)g(alignment)f(by)h(\256rst)164 1601
+y(de\256ning)11 b(some)g(dummy)g(sequences)i(in)e(the)g(block-\256le)g
+(that)g(have)h(letters)f(building)g(up)g(the)164 1661
+y(shape)f(of)f(the)h(histogram,)g(then)f(using)h(the)f(SURROUND)p
+1191 1661 V 18 w(CHARS)h(or)f(SHADE)p 1602 1661 V 18
+w(CHARS)164 1721 y(commands)f(together)g(with)g(the)g(SUB)p
+826 1721 V 18 w(CHARS)g(command)g(to)h(produce)e(the)i(desired)f(ef)o
+(fect.)164 1781 y(An)g(example)g(of)g(this)g(operation)g(being)g(used)g
+(to)g(show)g(fr)o(equencies)g(of)g(secondary)g(str)o(ucture)164
+1842 y(predictions)k(is)g(shown)h(in)f(example1.als)h(and)g(in)f(the)g
+(Protein)f(Engineering)h(paper)m(.)164 2010 y Fg(1)l(1)71
+b(Using)18 b(Colour)164 2121 y Fh(V)-6 b(ersion)12 b(1.4)h(includes)f
+(commands)g(to)g(allow)g(the)g(independent)g(colouring)f(of)h
+(characters,)164 2181 y(or)i(their)g(backgrounds.)24
+b(Colours)14 b(are)g(de\256ned)h(in)f(a)g(similar)g(manner)g(to)g
+(fonts)h(using)f(the)164 2242 y(DEFINE)p 344 2242 V 18
+w(COLOUR)f(command)f(\(American)g(spelling)g(also)h(allowed\).)k(For)12
+b(example:)164 2302 y(DEFINE)p 344 2302 V 18 w(COLOUR)h(7)g(1)f(0)g(0)
+164 2362 y(de\256nes)21 b(colour)f(number)h(7)g(to)f(be)h(red)g(-)g
+(see)g(Section)g(15.1)42 b(for)20 b(full)g(details)h(of)g(this)164
+2422 y(command.)26 b(Colours)16 b(99)f(and)g(100)g(are)g(pre-de\256ned)
+f(to)h(white)g(and)h(black.)27 b(ALSCRIPT)164 2482 y(assumes)13
+b(the)g(paper)f(colour)g(is)g(white.)949 2607 y(13)p
+eop
+%%Page: 14 15
+14 14 bop 164 315 a Fh(The)13 b(command)f(to)g(colour)g(the)g(text)g
+(of)g(a)h(character)f(or)g(text)g(string)g(is:)164 376
+y(CCOL)p 299 376 15 2 v 19 w(CHARS)164 436 y(the)g(command)g(to)g
+(colour)g(the)g(background)g(of)g(a)h(character)f(is)164
+496 y(SCOL)p 294 496 V 18 w(CHARS)164 556 y(both)g(have)g(similar)g
+(syntax)h(to)f(the)g(FONT)p 922 556 V 18 w(CHARS)h(command.)164
+616 y(COLOUR)p 371 616 V 19 w(REGION)7 b(and)g(COLOUR)p
+868 616 V 19 w(RES)g(have)g(similar)g(syntax)g(to)g(SHADE)p
+1581 616 V 20 w(REGION)164 677 y(and)12 b(SHADE)p 417
+677 V 18 w(RES.)164 737 y(An)g(example)h(command)e(\256le)i(that)f
+(uses)h(colour)f(is)g(shown)h(in)f(example3.als.)164
+906 y Fg(12)71 b(The)18 b(MASK)f(command)g(family)164
+1018 y Fh(The)f(idea)f(behind)g(the)h(MASK)f(command)g(is)g(to)h(build)
+f(up)g(a)g(set)h(of)f(character)g(positions)164 1078
+y(that)c(will)g(subsequently)g(be)h(boxed,)f(shaded,)i(set)e(in)g(a)h
+(particular)e(font,)h(etc.)18 b(For)11 b(example,)164
+1138 y(lets)h(say)h(we)f(want)g(to)g(box)f(the)h(most)g(frequently)f
+(occuring)h(character)f(at)h(each)h(position)e(in)164
+1198 y(an)h(alignment.)164 1259 y(The)h(command)164 1319
+y(mask)g(SETUP)164 1379 y(tells)f(ALSCRIPT)h(to)f(prepare)g(a)h(mask.)
+164 1439 y(mask)g(FRE)f(ALL)164 1499 y(speci\256es)h(that)f(the)h(most)
+f(frequently)f(occuring)h(character)g(at)g(each)h(position)f(in)g(the)h
+(align-)164 1559 y(ment)d(will)g(be)h(masked.)18 b(This)11
+b(command)f(can)g(be)h(restricted)f(to)g(a)h(region)e(of)h(the)h
+(alignment)164 1620 y(using:)21 b(mask)14 b(FRE)h(sx)f(sy)h(ex)f(ey)m
+(,)h(where)f(sx)g(etc)g(de\256ne)g(the)g(region)g(in)g(the)g(same)g
+(way)g(as)164 1680 y(for)e(font)p 319 1680 V 17 w(region)f(and)i(other)
+f(commands.)164 1740 y(mask)h(BOX)f(ALL)164 1800 y(T)m(ells)d(ALSCRIPT)
+g(to)g(create)f(the)h(boxing)f(lines)h(that)g(will)f(separate)h(the)g
+(masked)g(characters)164 1860 y(from)i(non-masked)h(characters)h(-)f
+(this)h(command)f(may)g(also)h(be)g(restricted)e(to)i(a)g(region)e(of)
+164 1921 y(the)h(alignment.)164 1981 y(The)h(mask)f(can)h(be)g(reset)f
+(for)g(re-use)g(using)g(the)g(command:)164 2041 y(mask)h(RESET)164
+2101 y(T)m(wo)f(further)g(commands)g(de\256ne)h(which)f(characters)h
+(can)f(be)h(used)g(when)g(calculating)f(the)164 2161
+y(mask.)25 b(This)15 b(allows)g(gap-characters,)g(or)f(other)g(amino)g
+(acids)h(to)f(be)h(excluded)g(from)e(the)164 2222 y(calculation)f(to)g
+(avoid)g(unwanted)g(boxing.)164 2282 y(mask)h(LEGAL)g("A)-6
+b(VLI")164 2342 y(de\256nes)11 b(the)g(A)-6 b(VL)10 b(and)h(I)f(as)i
+(the)e(only)h(characters)f(that)h(will)f(be)h(used)g(when)g
+(calculating)f(the)164 2402 y(mask.)164 2462 y(mask)j(ILLEGAL)g(".-)p
+556 2462 V 19 w(")949 2607 y(14)p eop
+%%Page: 15 16
+15 15 bop 164 315 a Fh(de\256nes)18 b(.-)h(and)p 464
+315 15 2 v 54 w(as)g(characters)f(that)g(will)g(not)g(be)g(used)h(when)
+f(calculating)g(the)g(mask.)164 376 y(NOTE:)d(the)f(blank)h(character)f
+(")g(")h(cannot)g(be)f(de\256ned)g(in)g(this)h(way)m(.)24
+b(T)m(o)15 b(avoid)f(boxing)g(")164 436 y(")g(characters)f(substitute)h
+(blanks)f(for)g(something)g(else)g(\(using)g(SUB)p 1382
+436 V 18 w(CHARS\),)h(calculate)164 496 y(the)e(mask,)h(then)g
+(substitute)f(back.)164 643 y Fb(12.1)59 b(Summary)15
+b(of)f(mask)i(commands)164 737 y Fh(mask)d(SETUP)f(#)h(Prepares)f(for)f
+(masking)164 797 y(mask)19 b(LEGAL)h Fe(<)p Fh(qstring)p
+Fe(>)e Fh(#)g(de\256nes)h(characters)g(to)f(include)g(in)h(ID)f(or)g
+(FRE)h(calcs)g(-)164 857 y(optional.)164 917 y(mask)c(ILLEGAL)g
+Fe(<)p Fh(qstring)p Fe(>)f Fh(#)g(de\256nes)h(characters)f(to)g
+(exclude)h(in)f(ID)g(or)g(FRE)g(calcs)h(-)164 978 y(optional.)164
+1038 y(mask)d(ID)f(ALL)i(N)f(#)f(Calculates)i(a)f(mask)f(that)h
+(\257ags)g(the)f(character)h(that)f(occurs)h(at)g(least)g(N)164
+1098 y(times)g(at)f(a)h(position.)18 b(The)12 b(word)f(ALL)i(can)f(be)f
+(substituted)h(by)g(four)e(numbers)i(that)f(de\256ne)164
+1158 y(a)i(region)e(of)h(the)h(alignment.)164 1218 y(mask)e(FRE)h(ALL)g
+(#)f(calculates)h(a)g(mask)f(that)g(\257ags)g(the)h(most)f(frequently)f
+(occuring)g(amino)164 1279 y(acid)i(at)h(each)f(position.)18
+b(ALL)13 b(may)g(be)f(replaced)g(by)g(four)g(numbers)g(de\256ning)f(a)i
+(region)e(of)164 1339 y(the)h(alignment.)164 1399 y(Multiple)c(mask)h
+(FRE)f(or)g(mask)h(ID)f(commands)g(may)g(be)h(applied,)g(using)g(dif)o
+(ferent)e(LEGAL)164 1459 y(and)i(ILLEGAL)i(character)e(de\256nitions.)
+17 b(In)9 b(this)h(way)f(more)g(complex)g(ef)o(fects)g(can)h(be)g
+(built)164 1519 y(up.)164 1579 y(The)h(mask)g(command)g(also)g(allows)g
+(characters)g(that)f(are)h(identical)f(to)h(one)g(sequence)g(to)g(be)
+164 1640 y(masked.)164 1700 y(mask)i(AGREE)g(ALL)g(N)164
+1760 y(will)e(mask)h(all)f(positions)h(that)f(are)h(identical)f(to)h
+(the)f(Nth)h(sequence.)18 b(Thus,)13 b(for)e(sequences)164
+1820 y(that)g(are)g(very)g(similar)g(to)g(a)h(newly)f(sequenced)h
+(sequence,)g(all)g(characters)f(identical)g(to)g(the)164
+1880 y(new)h(sequence)h(can)g(be)g(boxed)f(or)g(shaded,)h(or)f(set)h
+(in)f(a)g(dif)o(ferent)f(font)h(or)g(colour)g(etc...)164
+1941 y(mask)h(NOT)f(ALL)164 2001 y(allows)18 b(the)h(mask)f(to)h(be)f
+(inverted.)36 b(Thus,)21 b(all)d(positions)g(that)g(are)g(NOT)h(in)f
+(the)h(mask)164 2061 y(now)d(form)e(the)i(mask.)29 b(So,)17
+b(having)f(done)g(a)g(mask)g(AGREE,)h(a)f(mask)g(NOT)h(will)e(allow)164
+2121 y(the)h(positions)g(that)g(are)g(not)g(identical)g(to)g(the)g
+(selected)g(sequence)h(to)f(be)g(highlighted)f(or)164
+2181 y(substituted.)164 2242 y(mask)e(SUB)f(ALL)h Fe(<)p
+Fh(char)p Fe(>)164 2302 y Fh(substitutes)g(all)f(characters)g(in)h(the)
+f(mask)h(with)f(the)g(character)g Fe(<)p Fh(char)p Fe(>)p
+Fh(.)164 2362 y(mask)h(REGION)f(ALL)h(applies)g(a)g(mask)f(to)g(all)h
+(residues)f(in)h(the)f(de\256ned)g(region.)164 2422 y(The)h(following)e
+(ef)o(fects)h(can)h(now)f(be)h(applied)f(to)g(the)g(masked)h
+(characters:)164 2482 y(mask)g(BOX)f(ALL)h(#)g(boxes)g(the)f(masked)g
+(residues)h(-)f(ie)h(surrounds)f(them)g(by)g(lines.)949
+2607 y(15)p eop
+%%Page: 16 17
+16 16 bop 164 315 a Fh(mask)13 b(SHADE)f(ALL)h Fe(<)p
+Fh(grey)p Fe(>)f Fh(#)h(shades)g(the)f(masked)h(residues)f(by)h(grey)f
+(value.)164 376 y(mask)e(FONT)g(ALL)g Fe(<)p Fh(fontnum)p
+Fe(>)f Fh(#)g(Uses)i(font)e(fontnum)f(to)i(output)f(the)g(masked)h
+(residues.)164 436 y(mask)j(INVERSE)f(ALL)i(#)e(Inverts)g(the)g(masked)
+h(characters)f(-)g(ie)h(outputs)f(them)g(in)g(white.)164
+496 y(mask)21 b(CCOL)g(ALL)g Fe(<)p Fh(colnum)p Fe(>)f
+Fh(#)h(outputs)f(the)g(masked)h(characters)g(in)f(the)g(de\256ned)164
+556 y(colour)m(.)164 616 y(mask)11 b(SCOL)g(ALL)h Fe(<)p
+Fh(colnum)p Fe(>)f Fh(#)f(outputs)h(the)g(backgrounds)g(of)f(the)h
+(masked)g(characters)164 677 y(in)h(the)h(de\256ned)f(colour)m(.)164
+737 y(In)17 b(all)g(commands,)i(the)e(word)f(ALL)j(can)e(be)g(replaced)
+g(by)g(four)g(numbers)f(de\256ning)h(the)164 797 y(region)12
+b(to)g(which)g(the)g(command)g(is)h(applied.)164 857
+y(mask)g(RESET)g(#)g(resets)f(the)h(entire)f(mask)g(for)g(re-use)164
+1027 y Fg(13)71 b(Printing)17 b(ALSCRIPT)g(Files)164
+1138 y Fh(ALSCRIPT)i(produces)f(\256les)h(in)f(PostScript)g(which)g
+(may)h(be)f(printed)g(on)g(a)h(PostScript)164 1198 y(printer)14
+b(\(e.g.)25 b(an)15 b(Apple)g(LaserW)n(riter\).)24 b(If)14
+b(you)h(don')o(t)f(have)h(a)g(PostScript)e(printer)n(,)i(then)164
+1259 y(you)9 b(may)f(still)h(be)g(able)g(to)g(use)g(ALSCRIPT)g(if)g
+(you)f(get)h(hold)g(of)f(the)h(GhostScript)f(software.)164
+1319 y(This)j(is)f(a)g(free)g(package)g(that)g(interprets)g(PostScript)
+f(commands)h(and)g(can)g(produce)g(output)164 1379 y(on)g(a)g(lar)o(ge)
+g(number)f(of)h(dif)o(ferent)f(types)h(of)g(printer)m(.)16
+b(GhostScript)10 b(runs)g(on)g(most)g(hardware)164 1439
+y(types)e(\(including)g(PCs\))g(and)g(can)g(also)g(display)g(output)g
+(to)g(the)g(screen.)17 b(The)8 b(package)g(can)g(be)164
+1499 y(obtained)i(from)g(many)h(dif)o(ferent)e(sites)i(on)g(the)g
+(Internet)e(\(In)h(the)h(UK)g(try)f(src.doc.ic.ac.uk\).)164
+1559 y(The)k(actual)f(command)g(you)g(need)h(to)f(type)g(to)h(send)f(a)
+h(PostScript)e(\256le)i(to)f(the)g(printer)f(will)164
+1620 y(depend)g(on)h(your)e(system.)19 b(Consult)13 b(your)e(system)i
+(manager)f(for)g(help.)164 1680 y(Be)e(warned,)g(ALSCRIPT)f(can)h
+(create)f(extremely)g(lar)o(ge)g(PostScript)f(\256les)h(if)g(lots)h(of)
+f(boxing)164 1740 y(and)k(shading)g(is)h(done)f(on)g(big)g(alignments.)
+20 b(On)13 b(older)g(printers)f(such)i(output)f(may)g(take)g(a)164
+1800 y(long)f(time)g(to)g(process.)164 1970 y Fg(14)71
+b(Conclusion)164 2081 y Fh(ALSCRIPT)11 b(provides)f(a)h(powerful)f(set)
+h(of)f(formatting)g(and)g(editing)g(commands)h(speci\256c-)164
+2141 y(ally)h(tailored)g(for)g(multiple)f(sequence)i(alignments.)19
+b(It)12 b(is)h(best)f(used)h(in)g(conjunction)e(with)164
+2202 y(a)16 b(PostScript)f(previewer)h(such)g(as)h(Sun')m(s)f(PageV)m
+(iew)f(or)h(GhostV)m(iew)g(since)h(this)f(allows)164
+2262 y(the)g(ef)o(fect)g(of)f(changing)h(a)g(command)g(to)g(be)g(seen)h
+(quickly)m(.)28 b(In)16 b(the)g(absence)h(of)e(such)i(a)164
+2322 y(tool,)h(simpler)e(ef)o(fects)h(can)g(be)g(tested)g(out)g
+(without)f(destroying)g(too)h(many)f(trees)h(in)g(the)164
+2382 y(Laser)c(Printer!)949 2607 y(16)p eop
+%%Page: 17 18
+17 17 bop 164 315 a Fh(Like)12 b(most)f(programs,)g(ALSCRIPT)g(is)h
+(evolving)f(as)g(I)g(\256nd)g(new)g(problems)g(to)g(display)m(,)h(so)
+164 376 y(if)g(you)g(have)h(any)f(suggestions)h(-)f(I)g(shall)g
+(endeavour)g(to)h(include)f(them)g(in)g(a)h(later)f(version.)164
+545 y Fg(15)71 b(Appendices)164 671 y Fb(15.1)59 b(ALSCRIPT)16
+b(Command)e(Summary)164 765 y Fh(W)-6 b(ARNING:)17 b(V)-6
+b(ery)16 b(little)h(error)e(checking)i(is)g(performed)e(on)h(command)h
+(input.)30 b(If)16 b(you)164 825 y(give)d(the)f(wrong)h(number)f(of)g
+(ar)o(guments)g(to)h(a)g(command,)g(then)g(unexpected)f(things)h(may)
+164 885 y(happen,)i(or)f(the)h(program)e(will)h(crash)h(very)f
+(inelegantly)m(.)23 b(I)14 b(hope)h(to)f(\256x)g(this)g(in)h(the)f
+(next)164 945 y(version)f(of)g(the)h(program,)f(in)g(the)h(meantime,)g
+(make)f(sure)h(you)f(give)g(the)h(correct)f(number)164
+1006 y(of)f(ar)o(guments)g(to)g(each)h(command.)164 1066
+y(All)g(commands)h(up)f(to)h(the)f(\256rst)g(space)i(character)e(may)g
+(be)h(entered)f(in)h(UPPER)f(or)g(lower)164 1126 y(case)19
+b(or)e(MiXEd)i(case.)36 b(Quali\256ers)18 b(for)f(commands)h(\(e.g.)35
+b(REL\))19 b(must)f(be)g(written)f(in)164 1186 y(UPPER)12
+b(case.)164 1246 y(Command)g(Reference:)164 1361 y Fd(<int>)59
+b(=)30 b(enter)f(an)h(integer)59 b(\(e.g.)29 b(240\))164
+1421 y(<float>)g(=)h(enter)f(a)h(floating)f(point)g(number)g(\(e.g.)h
+(0.45\))164 1481 y(<string>)f(=)h(enter)f(a)h(string)f(\(e.g.)59
+b(ARNDql\))164 1541 y(<qstring>)29 b(=)h(enter)f(a)h(quoted)f(string)g
+(\(e.g.)g("Active)h(Site"\))164 1601 y(<char>)119 b(=)30
+b(enter)f(a)h(single)f(character.)164 1734 y Ff(15.1.1)50
+b(STEP)13 b(1)g(COMMANDS)164 1828 y Fh(These)18 b(all)f(refer)f(to)h
+(either)g(system)h(settings)f(-)g(e.g.)33 b(the)17 b(maximum)f(allowed)
+h(sequence)164 1888 y(length,)12 b(or)g(to)f(general)h(page)g(layout)g
+(features.)18 b(e.g.)g(the)12 b(longest)g(and)g(shortest)g(side)g(of)g
+(the)164 1948 y(paper)g(on)g(which)h(you)f(are)g(plotting.)164
+2081 y Ff(15.1.2)50 b(REQUIRED)13 b(STEP)g(1)g(COMMANDS)164
+2174 y Fh(BLOCK)p 335 2174 15 2 v 19 w(FILE)f Fe(<)p
+Fh(string)p Fe(>)164 2235 y Fh(Gives)18 b(the)g(name)g(of)f(the)h
+(\256le)f(that)h(contains)g(the)g(multiple)f(sequence)h(alignment)f(to)
+h(be)164 2295 y(formatted.)33 b(File)17 b(names)h(should)g(be)g(fully)e
+(quali\256ed)h(i.e.)35 b(not)18 b(relative)f(to)g(the)h(current)164
+2355 y(directory)m(.)k(If)13 b(no)h(block)g(\256le)f(command)h(is)g
+(given,)h(ALSCRIPT)f(will)f(expect)h(to)g(read)g(the)164
+2415 y(block)e(\256le)g(from)g(standard)g(input.)164
+2475 y(OUTPUT)p 363 2475 V 18 w(FILE)h Fe(<)p Fh(string)p
+Fe(>)949 2607 y Fh(17)p eop
+%%Page: 18 19
+18 18 bop 164 315 a Fh(De\256nes)14 b(the)f(output)g(\256le)g(name.)21
+b(This)14 b(command)e(should)i(be)f(near)g(the)h(beginning)e(of)h(the)
+164 376 y(command)f(list.)18 b(e.g.)h(OUTPUT)p 753 376
+15 2 v 19 w(FILE)12 b(Figure1.ps)164 436 y(Y)-5 b(ou)12
+b(MUST)h(de\256ne)f(an)h(output)f(\256le)g(unless)h(the)f(-p)g(option)g
+(\(See)g(Section)g(15.8)g(\))g(is)h(used.)164 496 y(DEFINE)p
+344 496 V 18 w(FONT)g Fe(<)p Fh(int)p Fe(>)e(<)p Fh(string)p
+Fe(>)h Fh(\()p Fe(<)p Fh(int)p Fe(>)p Fh(/DEF)l(AUL)-5
+b(T\)/\(REL)13 b Fe(<)p Fh(\257oat)p Fe(>)p Fh(\))164
+556 y(De\256nes)g(a)f(font)g(to)g(use)h(later:)k(e.g.)164
+658 y Fd(DEFINE_FONT)29 b(0)g(Helvetica)g(10)164 718
+y(DEFINE_FONT)g(2)g(Times-Roman)g(2)164 820 y Fh(de\256nes)15
+b(font)f(number)g(0)g(to)h(be)g(10)f(point)h(Helvetica,)g(and)g(font)f
+(number)g(2)h(to)f(be)h(2)f(point)164 880 y(T)n(imes-Roman.)29
+b(Font)16 b(0)g(is)g(always)g(used)h(as)f(the)g(default)g(font.)28
+b(Y)-5 b(ou)16 b(MUST)g(de\256ne)g(at)164 940 y(least)d(the)f(font)g(0)
+g(font.)164 1000 y(DEFINE)p 344 1000 V 18 w(FONT)h(3)f(T)n(imes-Roman)h
+(DEF)l(AUL)-5 b(T)164 1061 y(sets)16 b(font)f(3)g(to)g(be)h(T)n
+(imes-Roman)g(at)f(whatever)g(the)g(default)g(pointsize)g(is)h(as)g
+(set)g(by)f(the)164 1121 y(POINTSIZE)d(command.)164 1181
+y(DEFINE)p 344 1181 V 18 w(FONT)h(4)f(Helvetica)g(REL)i(0.5)164
+1241 y(sets)f(font)f(4)g(to)g(be)h(helvetica)f(at)h(half)e(the)i
+(default)f(pointsize.)164 1301 y(NOTE:)h(Font)f(names)h(must)f(be)g
+(written)g(exactly)g(as)h(shown)g(in)f(Section)g(15.3)h(.)164
+1362 y(SETUP)164 1422 y(Signals)f(the)g(end)h(of)f(the)g(STEP)h(1)f
+(commands.)164 1554 y Ff(15.1.3)50 b(OPTIONAL)13 b(STEP)h(1)e(COMMANDS)
+164 1648 y Fh(ADD)p 275 1648 V 18 w(SEQ)g Fe(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)164 1708 y Fh(Allows)20 b(extra)f(sequence)i
+(positions)f(to)f(be)h(created)g(in)g(an)g(existing)f(alignment.)40
+b(This)164 1769 y(permits)11 b(additional)g(annotations)g(to)h(be)f
+(interspaced)h(either)f(above,)h(below)m(,)g(or)f(anywhere)164
+1829 y(in)h(the)h(middle)e(of)h(an)h(alignment.)k(For)12
+b(example:)164 1889 y(ADD)p 275 1889 V 18 w(SEQ)g(0)h(10)164
+1949 y(would)f(create)g(an)h(additional)f(10)g(sequences)h(-)f(all)h
+(set)g(to)f(the)g(blank)g(character)g(before)g(the)164
+2009 y(\256rst)g(sequence)h(in)f(the)g(block)h(\256le)f(that)g(has)h
+(been)f(read)g(in.)164 2069 y(ADD)p 275 2069 V 18 w(SEQ)g(3)h(1)164
+2130 y(would)f(add)g(an)h(extra)f(sequence)h(after)f(sequence)h(3.)164
+2190 y(IMPOR)m(T)l(ANT)n(:)22 b(If)f(you)h(use)h(the)f(ADD)p
+916 2190 V 18 w(SEQ)g(facility)f(to)h(add)g(sequences)h(anywhere)164
+2250 y(except)d(after)e(the)i(last)g(sequence,)i(then)e(remember)e
+(that)i(the)f(sequence)h(numbers)f(will)164 2310 y(alter)m(.)43
+b(All)21 b(formatting)e(commands)h(that)h(follow)f(this)g(command)g
+(must)h(use)g(the)g(new)164 2370 y(sequence)13 b(numbering.)k(Thus)c
+(in)g(the)f(\256rst)g(example:)164 2431 y(ADD)p 275 2431
+V 18 w(SEQ)g(0)h(10)949 2607 y(18)p eop
+%%Page: 19 20
+19 19 bop 164 315 a Fh(what)20 b(was)h(sequence)g(number)e(1)h(becomes)
+h(sequence)g(1)n(1.)42 b(Sequences)20 b(1-10)g(are)g(the)164
+376 y(new)14 b(blank)g(sequences)h(to)f(be)g(used)h(for)e(annotation.)
+23 b(Note)14 b(that)g(the)g(sequence)g(numbers)164 436
+y(only)d(change)h(for)f(commands)h(AFTER)g(the)g(SETUP)g(command,)f
+(thus,)i(multiple)e(add)p 1702 436 15 2 v 17 w(seq)164
+496 y(commands)h(refer)g(to)g(the)g(sequence)h(number)f(as)h(implied)f
+(by)g(the)g(block)g(\256le.)164 556 y(POINTSIZE)g Fe(<)p
+Fh(int)p Fe(>)164 616 y Fh(De\256nes)f(the)h(pointsize)f(to)g(be)g
+(used)h(to)f(scale)h(the)f(plot)g(and)g(space)h(the)g(characters.)18
+b(Default)164 677 y(is)13 b(10)f(point.)164 737 y(NUMBER)p
+379 737 V 19 w(SEQS)164 797 y(If)k(present,)i(then)e(the)g(sequence)h
+(number)f(is)h(output)f(with)g(the)g(identi\256er)g(code.)31
+b(This)17 b(is)164 857 y(useful)12 b(for)g(\256nding)f(the)i
+(coordinates)f(of)g(residues)g(to)h(box)f(or)g(otherwise)g(highlight.)
+164 917 y(LANDSCAPE)164 978 y(Speci\256es)17 b(that)f(alignments)g
+(will)h(be)f(plotted)h(with)f(the)g(longest)h(paper)f(axis)h
+(horizontal.)164 1038 y(\(Can)12 b(get)h(longer)e(alignments)h(on)h(a)f
+(page)h(this)f(way\).)164 1098 y(POR)m(TRAIT)164 1158
+y(Speci\256es)h(that)h(alignments)f(will)g(be)h(plotted)f(with)g(the)h
+(longest)f(paper)g(axis)h(vertical)f(\(can)164 1218 y(get)f(more)g
+(sequences)i(on)e(a)g(page)h(this)f(way\).)164 1279 y(IDENT)p
+316 1279 V 18 w(WIDTH)h Fe(<)p Fh(int)p Fe(>)164 1339
+y Fh(Units)f(are)h(characters.)164 1399 y(Reserves)h
+Fe(<)p Fh(int)p Fe(>)e Fh(characters)h(at)g(left)g(of)g(every)f(page)h
+(for)g(plotting)f(identi\256ers.)19 b(Note)13 b(that)164
+1459 y(not)c(all)f(this)h(space)h(need)f(be)g(used,)i(if)d(a)h(smaller)
+g(pointsize)g(is)g(used)g(to)g(plot)f(out)h(the)g(identi\256er)164
+1519 y(codes,)k(than)g(is)f(used)h(for)f(the)g(main)g(alignment.)164
+1579 y(LINE)p 280 1579 V 18 w(WIDTH)p 464 1579 V 18 w(F)l(ACT)o(OR)i
+Fe(<)p Fh(\257oat)p Fe(>)164 1640 y Fh(V)-6 b(alue)15
+b(greater)e(than)h(0)g(that)g(scales)h(the)f(default)f(line)h(width.)23
+b(The)15 b(linewidth)e(is)h(obtained)164 1700 y(by)e(multiplying)f(the)
+i(pointsize)f(by)g(this)h(factor)m(.)164 1760 y(X)p 203
+1760 V 18 w(SP)-5 b(ACE)p 371 1760 V 18 w(F)l(ACT)o(OR)14
+b Fe(<)p Fh(\257oat)p Fe(>)164 1820 y Fh(Y)p 203 1820
+V 18 w(SP)-5 b(ACE)p 371 1820 V 18 w(F)l(ACT)o(OR)14
+b Fe(<)p Fh(\257oat)p Fe(>)164 1880 y Fh(This)f(determines)f(the)h
+(spacing)g(between)f(adjacent)h(residues)g(in)f(the)g(X)h(and)f(Y)h
+(directions.)164 1941 y(The)h(spacing)g(is)f(calculated)h(as:)20
+b(POINTSIZE)13 b(+)h(POINTSIZE)f(*)h(X)p 1408 1941 V
+18 w(SP)-5 b(ACE)p 1576 1941 V 18 w(F)l(ACT)o(OR)164
+2001 y(or)9 b(POINTSIZE)h(+)g(POINTSIZE)g(*)g(Y)p 851
+2001 V 17 w(SP)-5 b(ACE)p 1018 2001 V 19 w(F)l(ACT)o(OR)11
+b(as)f(appropriate.)16 b(Defaults)10 b(are)164 2061 y(0.2)j(and)f(0.0)h
+(respectively)m(.)164 2121 y(X)p 203 2121 V 18 w(SHIFT)p
+360 2121 V 17 w(F)l(ACT)o(OR)h Fe(<)p Fh(\257oat)p Fe(>)164
+2181 y Fh(Y)p 203 2181 V 18 w(SHIFT)p 360 2181 V 17 w(F)l(ACT)o(OR)g
+Fe(<)p Fh(\257oat)p Fe(>)164 2242 y Fh(These)h(determine)d(the)i(shift)
+f(relative)g(to)h(the)f(residue)h(drawing)e(position)i(that)f(is)h
+(given)f(to)164 2302 y(the)f(boxing)g(lines.)19 b(The)13
+b(shift)f(is)g(calculated)h(as)g(follows)164 2362 y(\(POINTSIZE)h(+)g
+(POINTSIZE)g(*)g(X)p 833 2362 V 18 w(SP)-5 b(ACE)p 1001
+2362 V 18 w(F)l(ACT)o(OR\))15 b(*)f(X)p 1317 2362 V 18
+w(SHIFT)p 1474 2362 V 17 w(F)l(ACT)o(OR)h(sim-)164 2422
+y(ilarly)d(for)f(Y)p 391 2422 V 18 w(SHIFT)p 548 2422
+V 17 w(F)l(ACT)o(OR.)164 2482 y(The)i(defaults)f(are)g(0.3)h(and)f(0.0)
+h(respectively)m(.)949 2607 y(19)p eop
+%%Page: 20 21
+20 20 bop 164 315 a Fh(Fiddling)10 b(with)h(the)g(X)p
+555 315 15 2 v 18 w(SP)-5 b(ACE/SHIFT)11 b(values)h(is)f(useful)h(to)f
+(\256ne)g(tune)g(the)g(appearance)g(of)164 376 y(the)h(alignment.)164
+436 y(MAX)p 283 436 V 18 w(INPUT)p 448 436 V 18 w(LEN)h
+Fe(<)p Fh(int)p Fe(>)164 496 y Fh(Units)h(are)g(characters.)23
+b(De\256nes)14 b(the)g(maximum)f(number)g(of)g(characters)h(possible)g
+(in)g(the)164 556 y(input)g(line)h(length.)25 b(This)16
+b(must)f(be)g(greater)f(than)h(the)f(maximum)g(number)h(of)f(sequences)
+164 616 y(\(MAX)p 300 616 V 18 w(NSEQ\).)164 677 y(e.g.)19
+b(MAX)p 373 677 V 18 w(INPUT)p 538 677 V 18 w(LEN)13
+b(600)164 737 y(Increases)g(the)f(default)g(value)g(of)g(500)g
+(characters)h(to)f(600)g(characters.)164 797 y(MAX)p
+283 797 V 18 w(NSEQ)h Fe(<)p Fh(int)p Fe(>)164 857 y
+Fh(Units)d(are)h(characters.)17 b(De\256nes)11 b(the)f(maximum)g
+(number)f(of)h(sequences)h(that)g(may)f(be)g(read)164
+917 y(by)g(the)h(program.)16 b(This)11 b(parameter)f(has)h(a)g(lar)o
+(ge)f(default)g(\(500\).)17 b(Y)-5 b(ou)10 b(may)g(need)h(to)f(reduce)
+164 978 y(it)i(on)g(computers)g(with)g(small)h(memories.)164
+1038 y(MAX)p 283 1038 V 18 w(ILEN)g Fe(<)p Fh(int)p Fe(>)164
+1098 y Fh(Units)e(are)f(characters.)18 b(The)11 b(maximum)f(length)g
+(allowed)h(for)f(a)g(sequence)i(identi\256er)d(code.)164
+1158 y(MAX)p 283 1158 V 18 w(SEQ)p 395 1158 V 18 w(LEN)k
+Fe(<)p Fh(int)p Fe(>)164 1218 y Fh(De\256nes)f(the)f(maximum)g(length)g
+(allowed)h(for)f(a)h(sequence)g(alignment)f(-)g(this)h(may)f(need)h(to)
+164 1279 y(be)g(reduced)h(from)e(the)h(8000)g(default)g(value)g(on)h
+(smaller)f(computers.)164 1339 y(X)p 203 1339 V 18 w(OFFSET)g
+Fe(<)p Fh(int)p Fe(>)g Fh(Units)h(of)f(points)g(\(1/72)f(inch\).)164
+1399 y(De\256nes)19 b(the)f(of)o(fset)g(along)g(the)g(X-axis)g(that)g
+(the)h(alignments)f(will)g(be)g(shifted)g(prior)f(to)164
+1459 y(printing.)35 b(Fiddle)17 b(with)h(this)h(value)f(to)g(get)g(a)g
+(nice)h(of)o(fset)f(from)f(the)h(bottom)f(left)h(hand)164
+1519 y(corner)12 b(of)g(the)g(page)g(if)g(your)g(page)h(size)f(is)h
+(not)f(A4.)164 1579 y(Y)p 203 1579 V 18 w(OFFSET)g Fe(<)p
+Fh(int)p Fe(>)g Fh(Units)h(of)f(points)g(\(1/72)f(inch\).)164
+1640 y(As)i(for)e(X)p 341 1640 V 18 w(OFFSET)l(,)i(only)f(Y)h(axis.)164
+1700 y(MAX)p 283 1700 V 18 w(SIDE)f Fe(<)p Fh(int)p Fe(>)g
+Fh(Units)h(of)f(inches.)164 1760 y(De\256nes)h(the)f(length)g(of)g(the)
+g(longest)h(side)f(of)g(the)h(printer)e(page.)164 1820
+y(MIN)p 264 1820 V 18 w(SIDE)h Fe(<)p Fh(int)p Fe(>)g
+Fh(Units)g(of)g(inches.)164 1880 y(De\256nes)h(the)f(length)g(of)g(the)
+g(shortest)h(side)f(of)g(the)h(printer)e(page.)164 1941
+y(VER)m(TICAL)p 409 1941 V 19 w(SP)-5 b(ACING)12 b Fe(<)p
+Fh(int)p Fe(>)164 2001 y Fh(De\256nes)h(the)f(vertical)g(spacing)h(in)f
+(character)h(units)f(between)h(blocks)f(of)g(sequences)i(when)164
+2061 y(more)e(than)g(one)g(block)h(will)f(\256t)g(on)g(a)g(page)h(-)f
+(default)g(is)g(0.)164 2121 y(DEFINE)p 344 2121 V 18
+w(COLOUR)h Fe(<)p Fh(int)p Fe(>)f(<)p Fh(\257oat)p Fe(>)g(<)p
+Fh(\257oat)p Fe(>)g(<)p Fh(\257oat)p Fe(>)164 2181 y
+Fh(DEFINE)p 344 2181 V 18 w(COLOR)164 2242 y(De\256nes)d(a)h(colour)e
+(-)h(the)g(\256rst)g(number)g(is)g(a)g(number)g(by)g(which)g(the)g
+(colour)g(will)g(be)g(referred.)164 2302 y(The)h(following)f(three)g
+(numbers)g(are)h(the)f(intensities)h(of)f(red,)i(green)e(and)g(blue)h
+(respectively)m(.)164 2362 y(Thus:)164 2422 y(DEFINE)p
+344 2422 V 18 w(COLOUR)j(1)g(0)f(0.2)h(0.8)949 2607 y(20)p
+eop
+%%Page: 21 22
+21 21 bop 164 315 a Fh(sets)19 b(colour)e(number)g(1)h(to)g(be)g(a)g
+(colour)g(with)f(no)h(red,)i(0.2)e(green)g(and)g(0.8)g(blue.)35
+b(The)164 376 y(exact)19 b(appearance)g(of)f(this)h(colour)f(will)g
+(depend)g(on)h(the)g(output)f(device.)37 b(If)18 b(you)g(\256nd)164
+436 y(suitable)d(combinations)f(of)h(colours)f(for)g(your)g(printer)n
+(,)h(then)g(please)g(let)g(me)g(know)f(and)h(I)164 496
+y(shall)e(distribute)e(your)h(suggestions)h(with)f(the)g(program.)164
+556 y(DO)p 239 556 15 2 v 18 w(TICKS)164 616 y(If)j(present,)i(then)f
+(tick)f(marks)h(are)f(drawn)h(below)f(the)h(numbers)f(at)h(the)g(top)f
+(of)h(the)f(page.)164 677 y(Otherwise)d(no)g(ticks)h(are)f(shown.)164
+737 y(NUMBER)p 379 737 V 19 w(INT)g Fe(<)p Fh(int)p Fe(>)164
+797 y Fh(Speci\256es)g(the)h(interval)e(for)h(writing)f(residue)h
+(position)g(numbers.)18 b(Default)12 b(is)h(10)164 857
+y(NO)p 239 857 V 18 w(NUMBERS)164 917 y(Switches)f(all)h(residue)f
+(numbering)f(of)o(f.)164 1050 y Ff(15.1.4)50 b(STEP)13
+b(2)g(COMMANDS)164 1144 y Fh(All)f(these)h(are)f(optional)g(formatting)
+f(commands.)164 1204 y(IMPOR)m(T)l(ANT)i(PLEASE)g(READ)g(THIS)f(NOTE:)
+164 1264 y(For)d(those)i(commands)f(that)f(accept)i(region)e
+(de\256nitions)h(\(e.g.)17 b(SURROUND)p 1547 1264 V 18
+w(CHARS\))10 b(it)164 1324 y(is)e(easiest)g(to)g(think)g(of)g(the)g
+(region)g(being)g(de\256ned)g(i)o(n)g(term)o(s)g(of)g(X)g(and)g(Y)f
+(coordinates,)f(where)164 1385 y(X)16 b(is)g(the)g(sequence)h(residue)f
+(coordinate)f(and)h(Y)g(is)g(the)g(sequence)h(number)e(coordinate.)164
+1445 y(Thus)h(3)f(7)f(means)i(the)f(3rd)f(residue)h(in)g(sequence)g(7.)
+26 b(3)15 b(7)g(12)g(42)g(means)g(the)g(rectangular)164
+1505 y(box)d(bounded)g(by)g(residue)h(3)f(of)g(sequence)h(7)f(and)h
+(residue)f(12)g(of)g(sequence)h(42.)164 1565 y(SURROUND)p
+441 1565 V 18 w(CHARS)f Fe(<)p Fh(string)p Fe(>)g Fh(ALL)164
+1625 y(Draw)g(lines)h(round,)f(but)g(not)g(between)g(the)h(characters)f
+(that)g(are)h(in)f(the)g(string.)18 b(e.g.)164 1685 y(SURROUND)p
+441 1685 V 18 w(CHARS)12 b(GP)h(ALL)164 1746 y(will)k(draw)f(lines)h
+(round)f(all)h(G)g(and)g(P)g(characters)g(in)g(the)g(alignment,)h(but)e
+(not)h(between)164 1806 y(adjacent)12 b(G)h(and)f(P)g(characters.)164
+1866 y(SURROUND)p 441 1866 V 18 w(CHARS)g Fe(<)p Fh(string)p
+Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)164 1926 y Fh(Similar)j(command,)i(but)f(the)g
+(surrounding)f(is)h(restricted)g(to)g(the)g(region)f(de\256ned)h(by)g
+(the)164 1986 y(four)11 b(integers.)164 2047 y(e.g.)164
+2107 y(SURROUND)p 441 2107 V 18 w(CHARS)h(IL)-5 b(VW)13
+b(3)g(12)f(7)g(32)164 2167 y(would)17 b(surround)f(IL)-5
+b(VW)18 b(characters)f(that)g(occur)g(in)g(the)g(region)g(de\256ned)g
+(from)f(residue)164 2227 y(positions)c(3-7)g(of)g(sequences)i(12)e(to)g
+(32.)164 2287 y(SHADE)p 333 2287 V 18 w(CHARS)g Fe(<)p
+Fh(string)p Fe(>)g Fh(ALL)i Fe(<)p Fh(\257oat)p Fe(>)164
+2348 y Fh(Shade)e(all)g(characters)h(in)f(the)g Fe(<)p
+Fh(string)p Fe(>)g Fh(by)g(the)h(grey)f(value)g(given)g(by)g
+Fe(<)p Fh(\257oat)p Fe(>)p Fh(.)18 b(e.g.)164 2408 y(SHADE)p
+333 2408 V 18 w(CHARS)12 b(GP)h(ALL)g(0.5)164 2468 y(would)f(shade)h
+(all)f(G)h(and)f(P)g(characters)g(in)h(the)f(alignment)g(by)g(the)g
+(grey)g(value)h(0.5.)949 2607 y(21)p eop
+%%Page: 22 23
+22 22 bop 164 315 a Fh(SHADE)p 333 315 15 2 v 18 w(CHARS)12
+b Fe(<)p Fh(string)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(\257oat)p
+Fe(>)164 376 y Fh(restricts)g(the)g(shading)h(to)f(the)g(region)g
+(de\256ned)g(by)h(the)f(four)f(integers.)18 b(Thus)164
+436 y(SHADE)p 333 436 V 18 w(CHARS)12 b(IL)-5 b(VW)13
+b(3)g(12)f(7)g(32)h(0.7)164 496 y(would)8 b(shade)g(I)g(L)g(V)g(and)g
+(W)g(characters)g(from)g(residues)g(3-7)g(of)g(sequences)g(12-32)g
+(inclusive)164 556 y(with)k(a)h(grey)f(value)g(of)g(0.7.)164
+616 y(FONT)p 297 616 V 18 w(CHARS)g Fe(<)p Fh(string)p
+Fe(>)g Fh(ALL)i Fe(<)p Fh(int)p Fe(>)164 677 y Fh(e.g.)164
+737 y(FONT)p 297 737 V 18 w(CHARS)e(GP)h(ALL)g(7)164
+797 y(would)j(use)h(font)e(7)i(to)f(write)f(out)i(all)f(G)g(and)g(P)g
+(characters.)31 b(Font)15 b(7)i(MUST)f(have)h(been)164
+857 y(de\256ned)12 b(using)g(the)h(DEFINE)p 697 857 V
+18 w(FONT)f(commands)h(above.)164 917 y(FONT)p 297 917
+V 18 w(CHARS)f Fe(<)p Fh(string)p Fe(>)g(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)164 978 y Fh(Similar)18 b(to)h(previous)g
+(command,)i(but)e(restricts)h(the)f(ef)o(fect)g(to)g(the)g(region)g
+(de\256ned)g(by)164 1038 y(the)d(\256rst)f(four)g(integers.)28
+b(The)16 b(font)f(must)h(have)g(been)g(de\256ned)f(by)h(the)g(DEFINE)p
+1638 1038 V 18 w(FONT)164 1098 y(command.)164 1158 y(e.g.)164
+1218 y(FONT)p 297 1218 V 18 w(CHARS)c(IL)-5 b(VW)13 b(3)g(45)f(9)g(70)h
+(7)164 1279 y(W)l(ould)c(set)h(the)f(font)f(to)h(7)h(for)e(I)h(L)h(V)f
+(and)g(W)h(characters)f(for)f(residues)i(3-9)e(of)h(sequences)h(45-)164
+1339 y(70)i(inclusive.)19 b(The)12 b(font)g(must)h(have)f(been)h
+(de\256ned)f(by)g(the)g(DEFINE)p 1416 1339 V 18 w(FONT)h(command.)164
+1399 y(FONT)p 297 1399 V 18 w(REGION)g Fe(<)p Fh(int)p
+Fe(>)e(<)p Fh(int)p Fe(>)h(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)164 1459 y Fh(De\256ne)g(the)h(font)e(to)h
+(use)h(throughout)e(the)i(region)e(speci\256ed)i(by)f(the)h(\256rst)f
+(four)f(integers.)164 1519 y(e.g.)164 1579 y(FONT)p 297
+1579 V 18 w(REGION)i(3)f(12)g(20)g(40)h(10)164 1640 y(Use)j(font)f(10)g
+(for)f(residues)i(from)e(residues)i(3-20)f(of)g(sequences)h(12-40.)26
+b(The)16 b(font)f(must)164 1700 y(have)d(been)h(de\256ned)f(using)g
+(the)h(DEFINE)p 910 1700 V 18 w(FONT)f(command.)164 1760
+y(FONT)p 297 1760 V 18 w(RESIDUE)h Fe(<)p Fh(int)p Fe(>)f(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 1820 y Fh(Set)j(the)h(font)e(for)
+h(use)h(with)f(a)g(single)h(residue)f(position)g(-)g(most)h(useful)f
+(when)h(used)f(with)164 1880 y(the)d(TEXT)i(command.)164
+1941 y(e.g.)164 2001 y(FONT)p 297 2001 V 18 w(RESIDUE)f(3)f(7)g(2)164
+2061 y(Use)i(font)g(2)f(for)g(residue)h(3)g(of)f(sequence)i(7.)23
+b(Font)13 b(2)h(must)g(have)g(been)g(de\256ned)f(using)h(the)164
+2121 y(DEFINE)p 344 2121 V 18 w(FONT)f(command.)164 2181
+y(LINE)g Fe(<)p Fh(string)p Fe(>)f(<)p Fh(int)p Fe(>)g(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 2242 y Fh(There)i(are)h(four)e
+(commands)h(of)g(this)g(type)g(for)f(drawing)h(horizontal)f(or)h
+(vertical)g(lines)g(on)164 2302 y(the)e(alignment.)164
+2362 y(LINE)h(LEFT)g Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)164 2422 y Fh(Draw)g(a)h(line)f(to)g(the)g
+(left)g(of)g(the)g(character)g(positions)h(indicated.)164
+2482 y(e.g.)949 2607 y(22)p eop
+%%Page: 23 24
+23 23 bop 164 315 a Fh(LINE)13 b(LEFT)g(3)g(12)f(24)164
+376 y(Draw)f(a)g(vertical)g(line)g(starting)g(at)g(residue)g(3)g(of)g
+(sequence)h(12)f(and)g(ending)g(at)g(residue)g(3)g(of)164
+436 y(sequence)i(24.)164 496 y(LINE)g(T)o(OP)g(3)f(12)g(24)164
+556 y(Draw)i(a)h(horizontal)f(line)h(above)f(the)h(character)f
+(positions)h(from)f(residue)g(3)h(of)f(sequence)164 616
+y(12)e(to)g(residue)h(24)f(of)g(sequence)h(12.)164 677
+y(Similar)e(commands)h(are:)164 737 y(LINE)f(BOTT)o(OM)h
+Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)f(<)p Fh(int)p
+Fe(>)g Fh(Draw)g(a)h(line)g(at)f(bottom)g(of)h(character)f(position.)
+164 797 y(LINE)j(RIGHT)f Fe(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
+Fe(>)g(<)p Fh(int)p Fe(>)g Fh(Draw)g(a)h(line)f(at)h(right)e(of)h
+(character)g(position.)164 857 y(BOX)p 272 857 15 2 v
+18 w(REGION)h Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)g(<)p
+Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)164 917 y Fh(Draw)h(a)h(box)f(around)
+g(the)g(region)g(indicated)g(by)g(the)g(four)g(integers.)164
+978 y(e.g.)164 1038 y(BOX)p 272 1038 V 18 w(REGION)h(2)f(5)g(30)h(7)164
+1098 y(W)l(ould)f(box)g(from)f(residue)i(2)f(of)g(sequence)h(5)f(to)h
+(residue)f(30)g(of)g(sequence)h(7.)164 1158 y(SHADE)p
+333 1158 V 18 w(REGION)g Fe(<)p Fh(int)p Fe(>)e(<)p Fh(int)p
+Fe(>)h(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(\257oat)p
+Fe(>)164 1218 y Fh(Shade)g(the)g(region)f(indicated)h(by)g(the)g
+(integers)g(with)g(the)g(grey)g(value)g(shown)g(by)g(the)g(\257oat.)164
+1279 y(e.g.)164 1339 y(SHADE)p 333 1339 V 18 w(REGION)h(30)f(40)g(35)g
+(46)h(0.2)164 1399 y(W)l(ould)f(shade)h(from)e(residue)i(30-35)e(of)h
+(sequences)i(40-46)d(with)h(a)h(grey)f(value)g(of)g(0.2.)164
+1459 y(SHADE)p 333 1459 V 18 w(RES)h Fe(<)p Fh(int)p
+Fe(>)f(<)p Fh(int)p Fe(>)g(<)p Fh(\257oat)p Fe(>)164
+1519 y Fh(Shade)g(just)h(one)f(amino)g(acid)g(with)g(the)h(grey)f
+(value.)164 1579 y(e.g.)164 1640 y(SHADE)p 333 1640 V
+18 w(RES)h(3)f(4)g(0.7)164 1700 y(Shades)h(residue)f(3)g(of)g(sequence)
+h(7.)19 b(\(Note:)e(this)12 b(can)h(also)g(be)f(achieved)g(with)g(the)
+164 1760 y(SHADE)p 333 1760 V 18 w(REGION)h(command,)f(but)g(requires)g
+(2)g(extra)g(numbers\))164 1820 y(TEXT)i Fe(<)p Fh(int)p
+Fe(>)e(<)p Fh(int)p Fe(>)g(<)p Fh(qstring)p Fe(>)164
+1880 y Fh(Place)g(the)h(text)f(string)g(at)g(the)g(location)g
+(indicated.)164 1941 y(e.g.)164 2001 y(TEXT)i(30)e(70)g("Active)h(Site)
+f(His")164 2061 y(would)k(put)g(the)g(text)f(Active)h(Site)g(His)h
+(starting)e(at)h(position)g(30)g(of)g(sequence)g(70.)30
+b(\(Use)164 2121 y(FONT)p 297 2121 V 18 w(RESIDUE)12
+b(or)g(FONT)p 721 2121 V 18 w(REGION)g(commands)g(to)g(set)g(the)g
+(font)f(of)h(the)f(text\).)18 b(T)m(ext)164 2181 y(added)13
+b(with)g(the)g(TEXT)i(command)e(will)g(not)g(be)g(split)g(across)h
+(page)f(breaks,)h(so)g(you)f(may)164 2242 y(in)d(some)h(circumstances)f
+(need)h(to)f(\256ddle)g(a)h(little)e(with)h(the)h(location/pointsize)e
+(for)h(the)g(text)164 2302 y(to)i(get)h(the)f(desired)g(result.)164
+2362 y(ID)p 220 2362 V 17 w(FONT)h(ALL)g Fe(<)p Fh(int)p
+Fe(>)164 2422 y Fh(Set)f(the)g(font)g(for)g(all)g(identi\256er)f(codes)
+i(to)f(the)h(font)e(number)h(shown)h(by)f Fe(<)p Fh(int)p
+Fe(>)p Fh(.)18 b(e.g.)164 2482 y(ID)p 220 2482 V 17 w(FONT)13
+b(ALL)g(3)949 2607 y(23)p eop
+%%Page: 24 25
+24 24 bop 164 315 a Fh(W)l(ould)12 b(set)h(all)f(the)g(identi\256er)g
+(codes)h(to)f(font)g(3.)164 376 y(ID)p 220 376 15 2 v
+17 w(FONT)h Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)164
+436 y Fh(Set)g(the)g(font)g(for)g(a)g(speci\256c)h(identi\256er)e(to)h
+(font)g(number)m(.)18 b(e.g.)164 496 y(ID)p 220 496 V
+17 w(FONT)13 b(12)f(4)164 556 y(Use)h(font)f(4)g(for)f(the)i(identifer)
+e(of)h(sequence)h(12,)g(default)e(font)h(for)g(all)g(other)g
+(identi\256ers.)164 616 y(SUB)p 264 616 V 18 w(CHARS)g(ALL)i
+Fe(<)p Fh(char)p Fe(>)e(<)p Fh(char)p Fe(>)164 677 y
+Fh(Substitute)g(the)g(characters)g(indicated.)164 737
+y(e.g.)164 797 y(SUB)p 264 797 V 18 w(CHARS)g(ALL)i(+)e(*)164
+857 y(would)g(change)g(all)h(occurences)f(of)g(+)h(to)f(*)h(in)f(the)g
+(alignment.)164 917 y(SUB)p 264 917 V 18 w(CHARS)g Fe(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p
+Fh(int)p Fe(>)g(<)p Fh(char)p Fe(>)g(<)p Fh(char)p Fe(>)164
+978 y Fh(restrict)g(the)g(substitution)g(to)g(the)h(region)e(shown.)164
+1038 y(e.g.)164 1098 y(SUB)p 264 1098 V 18 w(CHARS)h(1)h(1)f(7)g(8)h
+(\045)g(*)164 1158 y(would)e(substitute)h(*)g(for)f(\045)h(from)f
+(residue)h(1-7)f(of)g(sequences)i(1-8.)18 b(NOTE:)12
+b(T)m(o)g(substitute)164 1218 y(for)17 b(or)h(with)g(the)g(space)h
+(character)e(use)i(the)f(word)g(SP)-5 b(ACE.)19 b(e.g.)36
+b(to)18 b(change)g(all)g(space)164 1279 y(characters)12
+b(to)h(-.)164 1339 y(SUB)p 264 1339 V 18 w(CHARS)f(ALL)i(SP)-5
+b(ACE)12 b(-)164 1399 y(SUB)p 264 1399 V 18 w(ID)g Fe(<)p
+Fh(int)p Fe(>)g(<)p Fh(qstring)p Fe(>)164 1459 y Fh(Replace)h(the)f
+(numbered)g(identi\256er)f(by)h(the)h(string.)18 b(e.g.)164
+1519 y(SUB)p 264 1519 V 18 w(ID)12 b(34)g("Predicted)g(Secondary)g
+(Structure")164 1579 y(would)e(replace)h(whatever)f(the)h(identi\256er)
+e(of)i(sequence)g(34)g(was,)h(by)e(the)h(text)f(shown.)18
+b(This)164 1640 y(is)f(useful)f(when)g(used)h(in)f(conjunction)g(with)g
+(the)h(ADD)p 1185 1640 V 17 w(SEQ)g(command)f(shown)g(under)164
+1700 y(the)c(STEP)h(1)f(commands.)164 1760 y(INVERSE)p
+377 1760 V 18 w(CHARS)i Fe(<)p Fh(string)p Fe(>)f Fh(ALL/Range)i
+(\(similar)d(syntax)i(to)f(FONT)p 1524 1760 V 18 w(CHARS)h(but)164
+1820 y(no)e(font)g(number\))164 1880 y(Print)g(the)i(selected)f
+(characters)h(in)f(white.)21 b(This)14 b(clearly)f(will)g(only)g(work)g
+(if)f(you)i(\256rst)e(use)164 1941 y(the)f(SHADE)p 405
+1941 V 18 w(CHARS)g(command)g(to)g(shade)h(the)f(characters)g(with)g
+(something)g(other)f(than)164 2001 y(white.)164 2061
+y(CCOL)p 299 2061 V 19 w(CHARS)i Fe(<)p Fh(string)p Fe(>)g
+Fh(ALL)h Fe(<)p Fh(int)p Fe(>)164 2121 y Fh(Colour)f(all)g(characters)g
+(in)h(the)f Fe(<)p Fh(string)p Fe(>)g Fh(by)g(the)g(colour)g(de\256ned)
+g(by)g Fe(<)p Fh(int)p Fe(>)p Fh(.)164 2181 y(e.g.)164
+2242 y(CCOL)p 299 2242 V 19 w(CHARS)g(GP)g(ALL)i(12)164
+2302 y(would)c(colour)g(all)g(G)h(and)f(P)g(characters)h(in)f(the)h
+(alignment)e(by)i(the)f(colour)g(12.)18 b(This)11 b(colour)164
+2362 y(MUST)i(have)f(been)h(de\256ned)f(by)g(the)g(DEFINE)p
+1002 2362 V 19 w(COLOUR)h(command.)164 2422 y(CCOL)p
+299 2422 V 19 w(CHARS)f Fe(<)p Fh(string)p Fe(>)g(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 2482 y Fh(restricts)g(the)g
+(colouring)g(to)g(the)g(region)g(de\256ned)g(by)g(the)h(four)e
+(integers.)18 b(Thus)949 2607 y(24)p eop
+%%Page: 25 26
+25 25 bop 164 315 a Fh(CCOL)p 299 315 15 2 v 19 w(CHARS)12
+b(IL)-5 b(VW)13 b(3)g(12)f(7)g(32)g(7)164 376 y(would)21
+b(colour)f(I)h(L)h(V)f(and)h(W)f(characters)g(from)f(residues)i(3-7)f
+(of)f(sequences)j(12-32)164 436 y(inclusive)12 b(with)g(the)h(colour)e
+(7.)164 496 y(SCOL)p 294 496 V 18 w(CHARS:)e(This)h(has)g(identical)f
+(syntax)g(to)g(SCOL)p 1170 496 V 18 w(CHARS,)h(but)f(colours)g(the)g
+(back-)164 556 y(ground)j(of)f(the)i(character)n(,)f(rather)g(than)g
+(the)g(letter)g(itself.)164 616 y(COLOUR)p 371 616 V
+19 w(REGION)g Fe(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164
+677 y Fh(COLOR)p 335 677 V 19 w(REGION)164 737 y(Colour)j(the)g(region)
+g(indicated)f(by)i(the)f(integers)g(with)g(the)g(colour)g(number)f
+(given)h(as)h(the)164 797 y(last)d(number)m(.)164 857
+y(e.g.)164 917 y(COLOUR)p 371 917 V 19 w(REGION)f(30)h(40)f(35)g(46)g
+(2)164 978 y(W)l(ould)g(colour)g(from)f(residue)h(30-35)g(of)g
+(sequences)h(40-46)f(with)g(the)g(colour)g(2.)164 1038
+y(COLOUR)p 371 1038 V 19 w(RES)g Fe(<)p Fh(int)p Fe(>)g(<)p
+Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 1098 y Fh(Colour)g(just)g(one)h
+(amino)f(acid)g(with)g(the)g(de\256ned)g(colour)m(.)164
+1158 y(e.g.)164 1218 y(COLOUR)p 371 1218 V 19 w(RES)g(3)h(4)f(7)164
+1279 y(Colours)21 b(residue)f(3)h(of)g(sequence)g(7.)44
+b(\(Note:)34 b(this)21 b(can)g(also)h(be)f(achieved)g(with)f(the)164
+1339 y(COLOUR)p 371 1339 V 19 w(REGION)12 b(command,)h(but)f(requires)g
+(2)g(extra)g(numbers\))164 1486 y Fb(15.2)59 b(AMPS)16
+b(Block)e(\256le)g(format)164 1580 y Fh(The)f(\256rst)e(part)h(of)g(a)g
+(block-\256le)g(contains)g(the)g(identi\256er)f(codes)i(of)f(the)g
+(sequences)h(that)f(are)164 1640 y(to)g(follow)m(.)17
+b(Each)c(code)g(is)g(pre\256xed)e(by)i(the)f Fe(>)g Fh(symbol,)h(codes)
+g(must)f(not)g(contain)g(spaces.)164 1700 y(e.g.)164
+1802 y Fd(>HAHU)164 1862 y(>Trypsin)164 1922 y(>A0046)164
+1982 y(>Seq1)164 2144 y Fh(etc.)164 2204 y(ALSCRIPT)k(counts)f(the)h
+(number)e(of)h Fe(>)h Fh(symbols)f(in)g(the)h(beginning)e(of)h(the)h
+(\256le)f(until)g(a)164 2265 y(*)f(symbol)g(is)h(found.)23
+b(The)15 b(*)f(signals)h(the)f(beginning)f(of)h(the)g(multiple)g
+(alignment)f(which)164 2325 y(is)i(stored)f(VER)m(TICALL)-5
+b(Y)f(,)16 b(thus)e(columns)h(are)f(individual)f(sequences,)k(whilst)d
+(rows)g(are)164 2385 y(aligned)e(positions.)18 b(The)12
+b(*)g(symbol)g(must)g(lie)g(over)f(the)h(\256rst)g(sequence.)19
+b(A)12 b(further)e(star)i(in)164 2445 y(the)j(same)g(column)f(signals)h
+(the)g(end)f(of)g(the)h(alignment.)25 b(ALSCRIPT)15 b(uses)g(the)g
+(number)949 2607 y(25)p eop
+%%Page: 26 27
+26 26 bop 164 315 a Fh(of)13 b Fe(>)g Fh(symbols)h(at)g(the)f
+(beginning)g(of)g(the)g(\256le)h(to)f(work)g(out)g(how)g(many)h
+(columns)f(to)g(read)164 376 y(from)h(the)h(*)f(position.)26
+b(It)14 b(is)h(therefore)f(important)g(that)g(the)h(only)g
+Fe(>)g Fh(symbols)g(in)f(the)h(\256le)164 436 y(are)e(those)g(that)g
+(de\256ne)f(the)h(identi\256ers,)g(and)g(the)g(only)f(*)h(symbols)g
+(are)g(those)g(de\256ning)f(the)164 496 y(start)f(and)h(end)f(of)g(the)
+g(multiple)g(alignment.)17 b(The)12 b(block)f(\256le)g(can)h(contain)f
+(additional)g(text,)164 556 y(providing)16 b(that)i(there)f(are)h(no)f
+(more)g Fe(>)h Fh(or)f(*)h(symbols)f(in)h(the)f(\256le)h(than)f(those)h
+(used)g(to)164 616 y(de\256ne)12 b(the)g(identi\256ers)g(or)g
+(alignment)g(start)g(and)g(end.)164 677 y(A)g(simple,)h(small)g
+(block-\256le)e(is)i(shown)f(here.)164 791 y Fd(>Seq_1)164
+851 y(>A0231)164 911 y(>HAHU)164 971 y(>Four_Alpha)164
+1032 y(>Globin)164 1092 y(>GLobin_C)164 1152 y(*)164
+1212 y(ARNDLQ)164 1272 y(AAAAAA)164 1333 y(PPPPPP)164
+1393 y(PP)30 b(PPP)164 1453 y(WW)g(WWW)164 1513 y(LLLLLL)164
+1573 y(IIVVLL)164 1633 y(*)164 1781 y Fb(15.3)59 b(PostScript)14
+b(Fonts)164 1874 y Fd(Times-Roman,)164 1935 y(Times-Italic,)164
+1995 y(Times-Bold,)164 2055 y(Times-BoldItalic,)164 2115
+y(Helvetica,)164 2175 y(Helvetica-Oblique,)164 2236 y(Helvetica-Bold,)
+164 2296 y(Helvetica-BoldOblique,)164 2356 y(Courier,)164
+2416 y(Courier-Oblique,)164 2476 y(Courier-Bold)949 2607
+y Fh(26)p eop
+%%Page: 27 28
+27 27 bop 164 315 a Fd(Courier-BoldOblique,)164 376 y(AvantGarde-Book,)
+164 436 y(AvantGarde-BookOblique,)164 496 y(AvantGarde-Demi,)164
+556 y(AvantGarde-DemiOblique,)164 616 y(Bookman-Demi,)164
+677 y(Bookman-DemiItalic,)164 737 y(Bookman-Light,)164
+797 y(Bookman-LightItalic,)164 857 y(Helvetica-Narrow,)164
+917 y(Helvetica-Narrow-Bold,)164 978 y(Helvetica-Narrow-BoldOblique,)
+164 1038 y(Helvetica-Narrow-Oblique,)164 1098 y
+(NewCenturySchblk-Roman,)164 1158 y(NewCenturySchlbk-Bold,)164
+1218 y(NewCenturySchblk-Italic,)164 1279 y
+(NewCenturySchblk-BoldItalic,)164 1339 y(Palatino-Roman,)164
+1399 y(Palatino-Bold,)164 1459 y(Palatino-Italic,)164
+1519 y(Palatino-BoldItalic)164 1579 y(ZapfChancery-MediumItalic.)164
+1640 y(Symbol)164 1787 y Fb(15.4)59 b(386)15 b(DOS)g(installation)164
+1881 y Fh(IMPOR)m(T)l(ANT)d(-)e(The)i(programs)e(on)h(this)g(disk)h
+(will)e(ONL)-5 b(Y)12 b(WORK)f(on)g(a)g(PC)g(with)g(a)g(386)164
+1941 y(or)h(better)g(processor)m(.)18 b(See)13 b(the)f(T)m(echnical)g
+(Notes)h(section)g(for)e(details)i(of)f(why)m(.)164 2001
+y(Directions:)224 2115 y(1.)25 b(Create)12 b(a)h(directory)e(on)h(your)
+g(hard)g(disk.)19 b(e.g.)g(mkdir)11 b(ALSCRIPT)l(.)224
+2217 y(2.)25 b(Copy)12 b(the)h(Contents)f(of)g(the)g(\257oppy)g(disk)h
+(into)f(this)g(directory)m(.)405 2339 y Fd(e.g.)90 b(copy)29
+b(a:*.*)g(c:\\alscript.)224 2462 y Fh(3.)c(Edit)12 b(your)g(AUT)o
+(OEXEC.BA)-6 b(T)16 b(\256le)c(and)g(add)949 2607 y(27)p
+eop
+%%Page: 28 29
+28 28 bop 316 315 a Fd(C:\\ALSCRIPT)28 b(to)i(your)g(path.)224
+438 y Fh(4.)25 b(Edit)d(your)g(AUT)o(OEXEC.BA)-6 b(T)26
+b(\256le)c(and)g(add)g(the)h(following)e(two)h(lines.)49
+b(set)286 498 y(DOS4GVM=@ALSCRIPT)l(.VMC)14 b(set)e(DOS4G=quiet)164
+612 y(The)h(\256rst)f(line)g(is)g(an)g(instruction)g(to)g(read)g
+(instructions)g(from)f(the)h(\256le)g(ALSCRIPT)l(.VMC.)164
+672 y(This)k(sets)g(up)g(a)g(permanent)e(swap)i(\256le)g(on)f(your)g
+(hard)g(disk.)28 b(By)16 b(default,)g(the)f(swap)h(\256le)164
+733 y(is)d(about)g(12MBytes)h(in)f(size.)20 b(If)13 b(you)f(do)h(not)g
+(have)g(this)g(much)g(free)f(space)i(on)f(your)f(disk,)164
+793 y(then)j(edit)h(the)f(ALSCRIPT)l(.VMC)i(\256le)f(to)f(reduce)g(the)
+h(swap)g(\256le)f(size,)j(or)d(alternatively)m(,)164
+853 y(do)d(not)g(put)g(this)h(line)f(in)g(your)g(autoexec.bat.)164
+913 y(The)g(programs)f(will)g(run)f(without)h(this)h(swap)g(\256le,)f
+(but)g(you)h(will)f(be)g(limited)g(in)g(the)g(size)h(of)164
+973 y(alignment)e(you)h(can)g(process)h(by)f(the)g(amount)f(of)h(RAM)h
+(you)e(have)i(installed.)17 b(I)11 b(have)g(only)164
+1034 y(tested)i(this)f(program)g(on)g(a)h(486/33)f(with)g(8MBytes)h
+(RAM)g(and)f(a)h(386/33)f(with)g(4MBytes)164 1094 y(so)18
+b(I)g(do)f(not)h(know)f(the)h(practical)g(limitations)f(of)g(machines)h
+(with)f(smaller)h(memories.)164 1154 y(Any)12 b(feedback)g(would)g(be)h
+(appreciated.)164 1214 y(5.)46 b(T)m(ype)22 b(AUT)o(OEXEC.BA)-6
+b(T)24 b(to)e(initialise)f(the)h(changes,)j(or)c(better)g(still,)j
+(reset)e(the)164 1274 y(computer)m(.)164 1335 y(6.)17
+b(Y)-5 b(ou)10 b(should)g(now)g(be)g(able)g(to)f(run)h(all)f(three)h
+(programs)f(in)h(the)f(package)i(from)d(anywhere)164
+1395 y(on)13 b(your)f(disk.)19 b(msf2blc,)13 b(clus2blc)f(and)h
+(alscript.)19 b(If)12 b(you)g(get)h(memory)f(allocation)g(errors)164
+1455 y(when)20 b(you)g(try)g(to)g(run)f(alscript,)k(then)d(use)g(the)g
+(MAX)p 1182 1455 15 2 v 18 w(NSEQ)h(and)f(MAX)p 1559
+1455 V 18 w(SEQ)p 1671 1455 V 18 w(LEN)164 1515 y(commands)14
+b(to)f(reduce)g(the)h(default)f(limits.)22 b(If)13 b(the)g(program)g
+(still)g(won')o(t)g(run,)h(then)f(think)164 1575 y(about)f(buying)g
+(some)h(more)e(memory!!)164 1636 y(The)20 b(programs)f(msf2blc)h(and)g
+(clus2blc)g(should)f(run)h(OK,)g(but)g(if)f(you)h(try)f(to)h(process)
+164 1696 y(alignments)8 b(that)g(are)g(too)g(lar)o(ge)g(for)g(your)g
+(computer)n(,)f(you)h(may)g(get)g(a)g("malloc)g(error")g(which)164
+1756 y(will)14 b(stop)g(the)h(program.)23 b(If)14 b(this)g(happens)h
+(and)f(you)g(are)h(not)f(using)g(the)g(virtual)g(memory)164
+1816 y(option)j(discussed)h(above,)h(then)f(try)f(adding)g(the)g(line)g
+(set)h(DOS4GVM=@\256lename)f(to)164 1876 y(your)12 b(autoexec.bat)h
+(\256le.)20 b(If)12 b(you)g(don')o(t)g(have)h(enough)g(disk)g(space)g
+(to)g(do)f(this,)i(then)e(buy)h(a)164 1936 y(bigger)f(disk,)h(or)f
+(more)f(memory)m(.)164 2084 y Fb(15.5)59 b(TECHNICAL)15
+b(NOTES)164 2177 y Fh(The)i(executables)g(included)f(in)h(this)f
+(package)h(were)f(compiled)h(with)f(the)g(W)-6 b(A)g(TCOM)19
+b(C)164 2238 y(compiler)m(.)h(This)13 b(is)h(a)f(full)f(32)h(bit)g
+(compiler)f(that)h(makes)g(good)g(use)h(of)e(the)h(386)g(processor)164
+2298 y(and)j(does)h(not)f(work)f(on)h(the)g(16)g(bit)g(286.)30
+b(It)15 b(also)i(has)f(the)h(advantage)f(of)f(allowing)h(the)164
+2358 y(\257at)e(memory)f(model)h(to)g(be)h(used.)24 b(In)14
+b(practice)g(this)g(means)g(that)h(porting)e(programs)g(like)164
+2418 y(alscript)h(from)f(Unix)g(computers)h(like)f(the)h(Sun,)h(is)f
+(straightforward.)21 b(In)14 b(order)f(to)h(access)164
+2478 y(the)d(memory)f(of)h(the)g(computer)f(in)h(this)g(way)m(,)h(an)f
+(extra)g(program)f(called)h(a)h(dos)f(extender)g(is)949
+2607 y(28)p eop
+%%Page: 29 30
+29 29 bop 164 315 a Fh(required)9 b(-)h(this)h(is)g(called)f(DOS4GW)-5
+b(.EXE.)12 b(DOS4GW)e(is)h(automatically)e(invoked)h(every)164
+376 y(time)16 b(you)g(run)g(one)g(of)g(the)g(programs)g(and)g(is)h
+(responsible)f(for)g(managing)g(the)g(memory)164 436
+y(and)c(creating)g(the)h(swap)f(\256le)h(discussed)g(above.)164
+583 y Fb(15.6)59 b(Unix)15 b(Installation)164 677 y Fh(ALSCRIPT)c(is)h
+(distributed)e(with)h(executables)g(for)g(Sun)f(\(SunOS)g(4.1.3\),)i
+(Silicon)f(Graph-)164 737 y(ics)k(\(IRIX)f(5.3\),)i(DEC)g(ALPHA)f
+(OSF/1)f(and)h(Sun)f(Solaris)h(\(2.4\).)25 b(The)16 b(executables)f
+(are)164 797 y(stored)f(in)g(the)h(subdirectories)f(bin/sun,)h
+(bin/sgi,)g(bin/osf)f(and)g(bin/sol.)24 b(If)14 b(these)h(are)f(OK)164
+857 y(for)f(your)g(system,)h(then)g(just)f(add)h(the)f(apporpriate)g
+(directory)f(to)i(your)f(path,)h(or)f(put)g(links)164
+918 y(to)f(/usr/local/bin)g(or)f(somewhere)i(that)f(is)h(on)f(all)g
+(users)h(paths.)164 978 y(The)k(source)g(code)g(for)f(ALSCRIPT)i(is)f
+(contained)f(in)h(a)g(directory)f(hierarchy)m(.)31 b(The)17
+b(top)164 1038 y(directory)h(contains)g(a)h(README)i(\256le)d(and)h
+(the)f(BUILD)h(script.)38 b(Subdirectories)17 b(are:)164
+1098 y Ff(examples)12 b Fh(which)g(contains)g(example)f(command)g(and)h
+(alignment)f(\256les,)h Ff(doc)g Fh(which)f(con-)164
+1158 y(tains)16 b(L)286 1151 y Fa(A)307 1158 y Fh(T)329
+1174 y(E)354 1158 y(Xand)g(PostScript)e(copies)i(of)f(the)h(manual)f(-)
+g(a)h(subdirectory)f(of)g(this)h(contains)164 1218 y(an)j(HTML)g
+(version)g(of)f(the)g(manual,)i(and)f Ff(sr)o(c)g Fh(which)g(contains)f
+(the)h(source)f(code)h(and)164 1279 y(Make\256les)d(for)e(the)h
+(package.)27 b(There)15 b(may)g(also)g(be)h(a)f(directory)f(called)h
+Ff(bin)p Fh(.)26 b(If)14 b(present)164 1339 y(this)f(will)f(contain)g
+(subdirectories)g(with)h(executables)g(for)f(the)g(programs)g(in)h(the)
+f(package.)164 1399 y(Make\256les)j(to)f(build)g(alscript,)g(msf2blc,)h
+(clus2blc)f(and)h(alsnum)f(are)g(included)g(in)g(the)g
+Ff(sr)o(c)164 1459 y Fh(directory)m(.)37 b(V)-6 b(ersions)20
+b(for)f(Sun)f(\(acc)i(compiler)e(.sun\),)k(Silicon)c(Graphics)h
+(\(.sgi\),)i(DEC)164 1519 y(OSF/1)12 b(\(.osf\))f(are)i(included.)164
+1580 y(There)i(is)g(a)g(utility)e(csh)i(script)g(called)f(BUILD.)i
+(Simply)d(type)i(./BUILD)g(sun)g(to)f(compile)164 1640
+y(alscript)e(on)h(the)g(Sun,)g(./BUILD)g(sgi)g(for)f(Silicon)g
+(Graphics)h(or)f(BUILD)h(gcc)g(for)f(use)h(with)164 1700
+y(gcc)i(compiler)m(.)26 b(See)16 b(instructions)e(in)h(the)g(\256le)g
+(BUILD.)h(The)g(BUILD)f(script)g(will)g(create)164 1760
+y(a)e(/bin)f(directory)g(and)h(subdirecotry)f(if)g(not)h(already)g
+(present.)19 b(Y)-5 b(ou)13 b(can)g(create)g(make\256les)164
+1820 y(for)f(dif)o(ferent)f(computers)h(and)g(the)g(BUILD)h(script)f
+(should)g(still)h(function.)164 1968 y Fb(15.7)59 b(V)-8
+b(AX/VMS)16 b(Installation)164 2061 y Fh(The)c(standard)f(V)-6
+b(AX)10 b(C)i(compiler)e(is)h(not)g(ANSI.)g(Accordingly)m(,)g(ALSCRIPT)
+g(will)g(require)164 2122 y(changes)i(to)f(the)g(source)h(code)f(to)h
+(compile)f(on)g(a)g(V)-6 b(AX.)164 2182 y(The)12 b(DEC)g(C++)g
+(compiler)f(works)g(OK)g(for)g(alscript.)18 b(Alscript)11
+b(will)g(also)g(compile)g(on)h(Dec)164 2242 y(ALPHA)g(under)g(OpenVMS.)
+h(A)f(descrip.mms)h(\256le)f(is)h(included)f(for)f(this)i(purpose.)164
+2302 y Fc(W)m(ARNING:)g(I've)f(not)g(tested)h(V)-6 b(ersion)13
+b(2.0)g(of)f(ALSCRIPT)h(on)f(VMS)949 2607 y Fh(29)p eop
+%%Page: 30 31
+30 30 bop 164 315 a Fb(15.8)59 b(Alternative)13 b(ways)i(of)g(invoking)
+g(ALSCRIPT)164 409 y Fh(The)f(documentation)e(above)h(describes)h(the)f
+(interactive)f(mode)h(of)g(running)f(ALSCRIPT)l(.)164
+469 y(However)n(,)i(it)f(may)h(be)g(more)f(convenient)g(to)g(run)g(the)
+h(program)e(as)j(a)e(pipe)h(under)f(Unix)g(or)164 530
+y(MS-DOS.)f(Examples)h(are)f(shown)h(here.)164 590 y(ALSCRIPT)g(is)f(a)
+h(program)e(for)g(producing)g(pretty)h(versions)g(of)g(multiple)g
+(sequence)h(alig-)164 650 y(ments.)29 b(ALSCRIPT)16 b(will)f(also)h
+(format)f(single)h(sequences.)30 b(A)15 b(full)g(description)h(of)f
+(the)164 710 y(program)c(is)i(given)f(in)g(the)h(\256le)f
+("alscript.doc".)164 770 y(W)l(ays)h(of)f(running)f(alscript:)224
+884 y(1.)25 b(Interactive)13 b(mode:)21 b(just)13 b(type)h(alscript.)23
+b(Y)-5 b(ou)14 b(will)f(be)h(prompted)f(for)g(a)h(command)286
+945 y(\256le)h(name.)27 b(The)16 b(command)f(\256le)g(will)g(de\256ne)g
+(the)g(AMPS)g(bloc\256le,)h(and)f(name)g(of)286 1005
+y(the)d(\256le)g(to)h(store)f(the)g(PostScript)f(output)h(-)g(see)h
+(alscript.doc)g(for)e(details.)224 1107 y(2.)25 b(alscript)12
+b Fe(<)p Fh(command)p 683 1107 15 2 v 17 w(\256le)p Fe(>)g
+Fh(has)g(same)h(ef)o(fect)f(as)g(1,)h(But)f(does)h(not)f(prompt)f(for)g
+(the)286 1167 y(command)h(\256le)g(e.g.)19 b(alscript)12
+b(example1.als)224 1268 y(3.)25 b(alscript)13 b(-q)h
+Fe(<)f(<)p Fh(bloc\256le)p Fe(>)g(>)h(<)p Fh(PostScript)p
+Fe(>)f Fh(Quick)g(mode)h(-)f(uses)h(default)g(com-)286
+1329 y(mands,)g(reads)g(alignment)f(from)g(stdin,)h(writes)f
+(PostScript)g(to)g(stdout.)22 b(This)14 b(mode)286 1389
+y(creates)f(a)f(command)g(\256le)g(called)h(ALPSQ.COM.)286
+1470 y(e.g.)19 b(alscript)12 b(-q)g Fe(<)g Fh(example1.blc)h
+Fe(>)f Fh(example1.ps)224 1571 y(4.)25 b(alscript)12
+b(-f)g Fe(<)p Fh(command)p 729 1571 V 17 w(\256le)p Fe(>)g
+Fh(Similar)f(ef)o(fect)h(to)g(2.)224 1673 y(5.)25 b(alscript)16
+b(-f)g Fe(<)p Fh(command)p 737 1673 V 17 w(\256le)p Fe(>)g
+Fh(-s)h(Silent)e(operation:)25 b(No)17 b(messages)g(are)g(written)286
+1733 y(to)e(stderr)n(,)g(unless)g(fatal.)26 b(Silent)14
+b(operation)g(may)h(be)g(toggled)f(by)h(the)f(silent)p
+1657 1733 V 18 w(mode)286 1794 y(command)e(in)g(the)g(command)g
+(\256le.)224 1895 y(6.)25 b(alscript)8 b(-f)g Fe(<)p
+Fh(command)p 721 1895 V 18 w(\256le)p Fe(>)g Fh(-p)h
+Fe(<)f(<)p Fh(bloc\256le)p Fe(>)h(>)f(<)p Fh(PostScript)p
+Fe(>)g Fh(Make)h(alscript)286 1955 y(work)j(like)h(a)g(pipe)f(-)h
+(bloc\256le)f(is)h(read)g(from)e(stdin,)i(postscript)g(is)g(written)f
+(to)h(stdout.)286 2016 y(Messages)h(are)e(written)g(to)g(stderr)m(.)18
+b(T)m(o)13 b(supress)g(messages)g(include)f(the)h(-s)f(\257ag)g(too)286
+2097 y(e.g.)19 b(alscript)12 b(-f)g(example1.als)g(-p)g(-s)h
+Fe(<)f Fh(example1.blc)h Fe(>)f Fh(example1.ps)164 2211
+y(Using)f(alscript)g(as)h(a)f(pipe)g(has)h(the)f(advantage)g(of)g
+(allowing)g(the)g(bloc\256le)g(to)g(be)g(created)g(on)164
+2271 y(the)h(\257y)g(by)g(the)h(programs)e(msf2blc)h(or)g(clus2blc.)18
+b(For)12 b(example)g(if)g(we)g(have)h(a)f(GCG)h(.msf)164
+2331 y(\256le)d(called)g("pileup.msf")h(we)f(can)h(run)f(alscript)g
+(with)g(default)f(shading/fonts)h(and)g(send)h(the)164
+2391 y(results)h(straight)g(to)h(the)f(PostScript)f(printer)g("lpr")i
+(as)g(follows:)164 2451 y(msf2blc)f(-q)g Fe(<)p Fh(pileup.msf)g(|)g
+(alscript)g(-q)g(-s)h(|)f(lpr)949 2607 y(30)p eop
+%%Page: 31 32
+31 31 bop 164 315 a Fb(15.9)59 b(Pr)o(ogram)13 b(Crashes)i(and)g(Known)
+g(Bugs)164 409 y Fh(W)l(e've)10 b(used)h(ALSCRIPT)g(on)g(Sun)f(W)l
+(orkstations)g(and)h(Silicon)f(Graphics)g(for)g(some)h(time,)164
+469 y(with)i(very)f(lar)o(ge)h(alignments)g(and)g(command)g(\256les)g
+(with)g(thousands)g(of)g(commands.)20 b(All)164 530 y(seems)13
+b(to)f(work)g(OK,)h(the)f(program)g(has)g(not)h(crashed)f(on)g(us)h(at)
+g(all!!)164 590 y(However)n(,)f(the)g(command)f(interpreter)f(in)i
+(ALSCRIPT)g(is)g(very)g(simple)g(and)f(the)h(program)164
+650 y(will)f(crash)g(if)g(you)g(give)g(any)g(command)g(the)g(wrong)g
+(number)f(of)h(ar)o(guments)g(\(e.g.)18 b(leaving)164
+710 y(out)12 b(the)g(shade)h(value)g(in)f(a)g(shade)p
+761 710 15 2 v 19 w(chars)g(command\).)164 770 y(If)h(you)g(do)h(make)g
+(the)f(program)g(crash,)h(have)g(checked)g(all)f(the)h(documentation)f
+(and)h(your)164 830 y(numbers,)d(and)f(the)g(program)f(still)h
+(crashes.)19 b(Then)10 b(send)h(me)f(the)g(command)g(\256le)g(and)g
+(block)164 891 y(\256le)i(that)g(causes)i(the)e(crash)h(and)f(I)g(will)
+g(try)g(to)g(investigate.)164 951 y(Suggestions)g(for)g(improvements)f
+(to)h(the)h(program)e(are)h(always)h(welcome.)164 1098
+y Fb(15.10)59 b(W)o(ish)15 b(List)g(for)f(next)g(version!!)164
+1192 y Fh(A)d(command)f(interpreter)f(that)i(does)g(more)f(error)g
+(checking)g(will)g(be)h(included.)18 b(Currently)m(,)164
+1252 y(no)13 b(checking)g(is)g(done)g(to)g(make)g(sure)g(that)g(the)g
+(correct)g(number)f(of)g(ar)o(guments)h(are)g(given)164
+1312 y(to)f(a)h(command.)164 1372 y(Sequences)j(will)f(be)h(able)g(to)f
+(be)h(given)g(unique)f(labels)h(and)g(region)f(commands)g(refer)g(to)
+164 1433 y(these)c(labels)g(or)f(ranges)h(of)f(labels.)18
+b(This)12 b(will)e(permit)g(a)h(sequence)g(to)f(be)h(deleted)g(or)f
+(added)164 1493 y(to)i(the)h(alignment)e(without)h(having)g(to)g
+(update)g(the)h(.als)g(\256le.)164 1553 y(The)18 b(relative)f
+(numbering)f(option)g(will)h(be)h(extended)f(to)g(allow)g(numbering)f
+(relative)h(to)164 1613 y(a)f(position.)29 b(e.g.)h(456+7)16
+b(would)g(be)g(7)g(residues)g(after)g(position)g(456.)29
+b(This)17 b(will)e(allow)164 1673 y(annotation)9 b(of)g(positions)h
+(that)g(may)f(be)h(in)g(insertions)f(relative)h(to)f(the)h(reference)f
+(sequence.)164 1733 y(Special)h(TEXT)h(commands)f(will)g(be)g(extended)
+g(to)g(allow)g(alternative)f(shapes)i(to)f(be)g(drawn)164
+1794 y(and)i(scaled)h(in)f(various)h(ways.)164 1854 y(T)n(ree)21
+b(drawing)e(and)h(generalised)h(graphics.)41 b(An)20
+b(option)g(to)g(draw)g(arbitrary)f(lines)h(on)164 1914
+y(an)f(alignment)f(will)h(be)g(added.)39 b(This)19 b(will)g(permit)f
+(line)h(graphics)g(to)g(be)g(added)g(to)g(an)164 1974
+y(alignment.)d(The)8 b(initial)g(reason)g(for)g(this)g(will)g(be)g(to)g
+(show)g(dendrograms)g(\(trees\))g(alongside)164 2034
+y(the)k(alignment,)g(but)h(simple)f(line)g(graphs)g(could)g(also)h(be)g
+(plotted)e(under)h(the)h(alignment.)164 2095 y(Fiddle)c(factors)h(will)
+g(be)g(introduced)f(to)h(allow)g(\256ne)g(positioning)g(of)f
+(individual)h(characters.)164 2155 y(For)h(example,)h(if)e(you)i(like)f
+(your)g(\252I\272)g(characters)g(to)h(be)f(centred)g(rather)g(than)g
+(left)g(justi\256ed,)164 2215 y(this)h(will)g(be)h(possible.)164
+2275 y(In)h(single)p 342 2275 V 18 w(page)h(mode,)h(it)e(will)g(be)h
+(possible)g(to)g(add)g(arbitrary)e(text)h(to)h(an)g(alignment)f(for)164
+2335 y(\256nal)e(annotation,)g(e.g.)19 b(titles)12 b(etc.)164
+2396 y(V)-6 b(ariable)12 b(height/width)g(sequence)h(lines)f(will)g(be)
+h(permitted)e(\(maybe\).)949 2607 y(31)p eop
+%%Page: 32 33
+32 32 bop 164 315 a Fb(15.1)m(1)59 b(Acknowledgements)164
+409 y Fh(I)19 b(thank)g(all)h(those)g(who)f(have)h(emailed)f(me)h(with)
+f(suggestions)h(for)e(improvements)h(to)164 469 y(alscript.)e(I've)10
+b(tried)g(to)g(include)h(some)f(of)g(these)h(in)g(the)f(current)g
+(distribution)f(\(e.g.)18 b(screen-)164 530 y(ing\).)164
+677 y Fb(15.12)59 b(Refer)o(ences)164 831 y Fd(1.)h(Barton,)29
+b(G.)g(J.)h(\(1993\),)164 891 y("ALSCRIPT)f(A)h(tool)f(to)h(format)f
+(multiple)g(sequence)g(alignments",)164 951 y(Protein)g(Engineering,)59
+b(Volume)29 b(6,)g(No.)h(1,)g(pp.37-40.)164 1071 y(2.)60
+b(Barton,)29 b(G.)g(J.)h(\(1990\),)313 1132 y("Protein)f(Multiple)g
+(Sequence)g(Alignment)g(and)h(Flexible)f(Pat-)164 1192
+y(tern)g(Matching",)164 1252 y(Methods)g(in)h(Enzymology,)313
+1312 y(183,403-428.)164 1433 y(3.)60 b(Barton,)29 b(G.)g(J.)h(and)g
+(Sternberg,)e(M.)i(J.)g(E.)f(\(1987\),)313 1493 y("A)h(Strategy)f(for)h
+(the)f(Rapid)g(Multiple)g(Alignment)g(of)h(Pro-)164 1553
+y(tein)f(Sequences:)433 1613 y(Confidence)g(Levels)g(From)g(Tertiary)g
+(Structure)g(Comparisons",)164 1673 y(Journal)g(of)h(Molecular)f
+(Biology,)313 1733 y(198,327-337)164 1854 y(4.)h(Higgins,)f(D.)g(G.)h
+(and)g(Sharp,)f(P.)g(M.)h(\(1989\),)313 1914 y("Fast)g(and)f(sensitive)
+g(multiple)g(sequence)g(alignments)g(on)h(a)f(microcomputer",)164
+1974 y(CABIOS,)313 2034 y(5,151--153)164 2155 y(5.)h(Devereux,)f(J.)g
+(Haeberli,)g(P.)h(Smithies,)f(O.)g(\(1984\),)313 2215
+y("A)h(comprehensive)f(set)g(of)h(sequence)f(analysis)g(programs)g(for)
+g(the)h(VAX",)164 2275 y(Nucleic)f(Acids)g(Res.)313 2335
+y(12,)h(387-395)164 2456 y(6.)g(Livingstone,)e(C.)i(D.)g(and)f(Barton,)
+g(G.)h(J.)f(\(1993\),)949 2607 y Fh(32)p eop
+%%Page: 33 34
+33 33 bop 164 315 a Fd("Protein)29 b(Sequence)g(Alignments:)58
+b(A)30 b(Strategy)f(for)h(the)f(Hier-)164 376 y(archical)g(analysis)164
+436 y(of)h(residue)f(conservation")164 496 y(Computer)g(Applications)g
+(in)g(the)h(Biosciences,)164 556 y(9,)g(745-756.)949
+2607 y Fh(33)p eop
+%%Trailer
+end
+userdict /end-hook known{end-hook}if
+%%EOF