JPRED-2 Add alscript to the Git repository
[jpred.git] / sources / alscript / doc / alscript.ps
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218 1800 y(LEASE)f(VERSION.)164 1860 y(Version)g(1.4.2)g(15)h(February)f
219 (1993:)g(Make)h(silent_mode)e(toggle.)164 1921 y(Version)h(1.4.3)59
220 b(1)30 b(March)119 b(1993:)29 b(Fix)h(bug)f(in)h(colour)f(option.)164
221 1981 y(Version)g(1.4.4)g(24)h(March)119 b(1993:)29 b(Add)h(mask)f
222 (features)g(\(should)g(be)h(ver-)164 2041 y(sion)f(1.5\).)164
223 2101 y(Version)g(1.4.5)g(25)h(May)179 b(1993:)29 b(Include)g(alsnum)h
224 (program)f(in)g(distribution.)373 2161 y(7)h(June)149
225 b(1993:)29 b(Fix)h(NO_NUMBERS)f(bug)g(in)h(documentation)1120
226 2222 y(Change)g(defaults)f(for)g(-q)h(op-)164 2282 y(tion)f(to)h(use)g
227 (MASK.)164 2402 y(Version)f(2.0)89 b(23)30 b(May)119
228 b(1995:)30 b(Numerous)f(changes)g(and)g(addi-)164 2462
229 y(tions)g(including)g(the)961 2607 y Fh(2)p eop
230 %%Page: 3 4
231 3 3 bop 164 315 a Fd(option)29 b(to)h(colour)f(backgrounds)164
232 376 y(differently,)g(ommission)f(of)i(idents)f(on)164
233 436 y(second)g(and)h(subsequent)f(lines,)g(helix,)164
234 496 y(strand)g(and)h(other)f(special)g(characters,)164
235 556 y(relative)g(numbering,)g(error)g(checking)g(of)164
236 616 y(ranges)g(on)h(input,)f(bounding)g(box,)164 677
237 y(screening,)g(conservation)f(colouring...)164 737 y(Version)h(2.03)89
238 b(5)30 b(June)149 b(1996:)29 b(Small)h(bug)f(fixes)h(-)f(patches)g
239 (incorporated.)164 797 y(BACKGROUND_REGION)f(and)i(BOUNDING_BOX)e
240 (commands)h(moved)g(to)164 857 y(step)g(1)h(section.)164
241 1087 y Fg(2)72 b(Read)17 b(This)g(First)h(-)g(VERSION)e(2.0)164
242 1198 y Fh(This)d(manual)f(describes)h(an)g(interim)e(release)i(of)f
243 (ALSCRIPT)h(that)g(includes)f(many)h(addi-)164 1259 y(tional)c
244 (features)g(over)g(the)h(previously)f(distributed)f(V)-6
245 b(ersion)10 b(1.4.5.)18 b(I)9 b(had)h(hoped)f(to)g(make)h(a)164
246 1319 y(lot)h(more)g(changes)h(and)f(improvements)g(before)g
247 (distributing)f(the)h(new)h(version,)f(however)164 1379
248 y(I)16 b(have)h(not)g(had)f(the)h(time)f(to)h(do)f(this.)32
249 b(I)16 b(am)h(distributing)e(V)-6 b(ersion)17 b(2.0)g(since)g(the)g
250 (new)164 1439 y(features)e(have)g(been)h(used)f(in)g(a)h(number)e(of)h
251 (published)g(alignment)g(\256gures.)27 b(Please)15 b(see)164
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253 (features.)164 1669 y Fg(3)72 b(Related)17 b(Pr)o(ograms)164
254 1780 y Fh(The)12 b(AMPS)g(package)g(\(Barton,)g(1990\).)17
255 b(This)c(performs)e(multiple)g(sequence)h(alignments)164
256 1840 y(and)g(databank)h(scanning.)164 1901 y(AMAS)h(\(Livingstone)f
257 (and)g(Barton,)h(1993,)g(CABIOS,)g(9,)g(745-756\).)21
258 b(Analysis)14 b(of)f(Mul-)164 1961 y(tiply)h(Aligned)f(Sequences.)24
259 b(This)15 b(package)f(uses)h(a)g(sophisticated)f(set-based)h(method)e
260 (to)164 2021 y(identify)e(patterns)i(of)f(residue)g(conservation)g(in)g
261 (multiple)g(sequence)h(alignments.)164 2081 y(All)k(programs)f(are)h
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263 b(Please)164 2141 y(see)11 b(the)g(README)h(\256le)f(for)f(details)h
264 (licencing)f(and)h(registration.)17 b(Y)-5 b(ou)10 b(can)h(read)g
265 (manuals)164 2202 y(for)h(the)g(programs)f(and)i(some)f(related)g
266 (papers)h(at)f(http://geof)o(f.biop.ox.ac.uk/.)961 2607
267 y(3)p eop
268 %%Page: 4 5
269 4 4 bop 164 315 a Fg(4)72 b(A)-5 b(vailability)164 427
270 y Fh(ALSCRIPT)9 b(is)g(available)f(free)g(of)g(char)o(ge)g(for)g
271 (academic)h(and)f(non-commercial)f(purposes.)164 487
272 y(Distribution)16 b(is)i(by)f(anonymous)g(ftp)f(from)h(geof)o
273 (f.biop.ox.ac.uk.)33 b(See)17 b(the)h(README)164 547
274 y(\256le)f(on)g(the)g(ftp)f(server)h(for)f(details.)33
275 b(Y)-5 b(ou)17 b(need)g(to)g(register)g(with)f(G.)i(J.)g(Barton)f
276 (before)164 608 y(downloading)12 b(the)g(software.)164
277 777 y Fg(5)72 b(Installing)17 b(ALSCRIPT)164 889 y Fh(See)12
278 b(the)h(appropriate)e(section)i(for)e(the)h(computer)g(type)g(you)g
279 (are)h(using:)164 949 y(For)g(PCs)i(see)f(see)h(Section)f(15.4.)23
280 b(For)14 b(Unix)f(see)i(see)g(Section)e(15.6)i(.)23 b(For)13
281 b(VMS)i(see)f(see)164 1009 y(Section)e(15.7)g(.)164 1178
282 y Fg(6)72 b(Brief)17 b(Description)f(of)i(ALSCRIPT)164
283 1290 y Fh(ALSCRIPT)c(takes)h(a)f(multiple)f(sequence)i(alignment)e(in)h
284 (AMPS)g(\(Barton)f(&)h(Sternber)o(g,)164 1350 y(1987,)23
285 b(Barton,)f(1990\))e(block-\256le)f(format)h(and)g(a)h(set)g(of)f
286 (formatting)f(commands)h(and)164 1410 y(produces)e(a)h(PostScript)f
287 (\256le)g(that)g(may)h(be)g(printed)e(on)i(a)g(PostScript)e(laser)i
288 (printer)n(,)g(or)164 1470 y(viewed)8 b(using)g(a)g(PostScript)g
289 (previewer)g(\(e.g.)16 b(Sun)8 b(Microsystem')m(s)g(PageV)m(iew)g
290 (program\).)164 1531 y(CLUST)l(AL)i(and)f(GCG)g(format)e(multiple)h
291 (alignment)g(\256les)h(may)f(also)h(be)g(used)g(\(see)g(below\).)164
292 1591 y(ALSCRIPT)h(is)h(NOT)g(a)f(multiple)f(sequence)i(alignment)e
293 (program,)h(nor)g(is)g(it)g(an)h(alignment)164 1651 y(editor)m(.)164
294 1711 y(Given)k(a)g(block-\256le)f(and)h(pointsize)g(\(character)f
295 (width/height\),)g(ALSCRIPT)h(calculates)164 1771 y(how)g(many)g
296 (residues)h(can)f(be)h(\256tted)f(across)h(the)f(page,)h(and)g(how)f
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298 (then)h(prints)g(the)g(alignment)f(at)h(the)g(chosen)g(pointsize)g(on)g
299 (as)g(many)164 1892 y(pages)h(as)g(are)g(needed.)22 b(Running)13
300 b(ALSCRIPT)h(with)f(a)h(smaller)f(or)g(lar)o(ger)g(pointsize)g(will)164
301 1952 y(automatically)f(re-scale)g(the)h(alignment)f(to)g(\256t)g(on)g
302 (fewer)g(or)h(more)e(pages)j(as)f(appropriate.)164 2012
303 y(The)i(actual)f(page)h(dimensions)f(may)h(be)f(re-set)g(to)g(any)h
304 (value,)g(so)g(if)f(you)g(have)g(access)i(to)164 2072
305 y(an)11 b(A3)g(PostScript)f(printer)n(,)h(or)g(typesetting)g(machine,)g
306 (alignments)g(can)h(readily)e(be)h(scaled)164 2133 y(to)h(maximise)g
307 (the)h(available)f(space.)164 2193 y(Each)j(output)g(page)g(has)g
308 (three)g(basic)g(regions.)26 b(The)15 b(left)f(hand)h(edge)g(contains)g
309 (identi\256er)164 2253 y(codes)f(for)e(each)i(sequence.)22
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312 (tick)h(marks.)17 b(ALSCRIPT)10 b(commands)g(make)f(use)h(of)164
313 2373 y(a)k(character)g(coordinate)f(system)i(for)e(font)g(changes,)j
314 (and)e(other)f(formatting)g(commands.)164 2433 y(Thus,)d(any)f(residue)
315 f(in)g(the)g(alignment)g(may)g(be)g(referred)f(to)h(by)g(its)h
316 (sequence)g(position)f(num-)961 2607 y(4)p eop
317 %%Page: 5 6
318 5 5 bop 164 315 a Fh(ber)13 b(\(x-axis\))f(and)h(sequence)h(number)e
319 (\(y-axis\),)h(similarly)m(,)g(ranges)g(of)f(residue)i(positions,)164
320 376 y(or)e(sequences)h(may)g(also)f(be)h(de\256ned)f(in)g(the)g
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322 (commands)h(allow)f(the)g(following)f(functionality:)164
323 496 y(Fonts:)28 b(Any)18 b(PostScript)f(font)g(at)h(any)g(size)g(may)g
324 (be)g(de\256ned)f(and)h(used)g(on)g(individual)164 556
325 y(residues,)13 b(regions)f(or)g(identi\256er)f(codes.)164
326 616 y(Boxing:)16 b(Simple)8 b(rectangular)h(boxes)g(may)g(be)g(drawn)g
327 (around)g(any)g(part)f(of)h(the)g(alignment.)164 677
328 y(Particular)i(residue)g(types)h(may)g(be)g(selected)g(and)g
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330 (if)g(the)f(characters)h('G')f(and)g('P')g(are)g(selected,)j(then)d
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332 (characters,)h(but)e(only)h(where)g(G)h(and)f(P)g(border)f(with)h
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334 b(shading)g(of)f(any)h(level)g(from)f(black)g(to)h(white)g(may)g(be)g
335 (applied)f(to)h(any)164 917 y(region)k(of)h(the)g(alignment,)i(either)d
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338 (positions)f(6)h(and)f(30")164 1038 y(T)m(ext:)23 b(Speci\256c)14
339 b(text)h(strings)g(may)g(be)g(added)g(to)g(the)g(alignment)f(at)h(any)g
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341 1158 y(Lines:)22 b(Horizontal)13 b(or)h(vertical)g(lines)g(may)g(be)g
342 (drawn)g(to)g(the)g(left,)h(right,)f(top)g(or)g(bottom)164
343 1218 y(of)e(any)g(residue)h(position)f(or)g(group)f(of)h(positions.)164
344 1279 y(Colour:)17 b(Characters)c(or)f(character)g(backgrounds)g(may)g
345 (be)g(independently)g(coloured.)164 1339 y(The)e(example)e(block)h
346 (\256le)g("example1.blc")h(and)f(command)g(\256le)f("example1.als")j
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348 1459 y(Although)7 b(written)g(with)g(the)g(aim)g(of)g(producing)g
349 (\256gures)g(for)g(journal)g(submission,)h(ALSCRIPT)164
350 1519 y(may)i(be)h(used)g(as)g(a)f(tool)g(for)g(interpreting)f(multiple)
351 g(sequence)j(alignments.)17 b(For)10 b(example,)164 1579
352 y(the)h(boxing,)h(shading)g(and)f(font)g(changing)g(facilities)h(can)f
353 (be)h(applied)f(to)h(highlight)e(amino)164 1640 y(acids)h(of)f(a)g
354 (particular)g(type)g(and)h(thus)f(draw)g(attention)g(to)g(clusters)h
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363 2161 y(where)i(one)f(character)h(is)g(seen)g(in)g(more)f(than)h(N)f(of)
364 h(the)f(sequences.)20 b(It)11 b(is)h(also)g(possible)g(to)164
365 2222 y(box/shade)d(etc)g(the)f(most)h(frequently)e(occurring)h
366 (character)g(at)h(each)g(position.)17 b(Commands)164
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373 y(sequence)h(in)f(the)h(set.)18 b(See)13 b(the)f(section)h(on)f(MASK)g
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375 %%Page: 6 7
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381 (physico-chemical)g(properties)g(of)g(the)g(amino)164
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387 677 y(set-based)13 b(approach)f(to)g(this)g(problem.)164
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390 b(1.4.5)h(includes)f(the)f(program)g("alsnum".)38 b(This)20
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399 1319 y(position)d(rather)g(than)g(the)g(alignment.)164
400 1379 y(T)m(o)g(use)h(the)f(program:)164 1439 y(1.)31
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407 y(2.)18 b(Decide)13 b(what)f(is)h(the)f(number)f(of)h(the)g(\256rst)g
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411 b(Decide)13 b(the)f(numbering)f(interval)h(\(e.g.)19
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413 b(Run)13 b(the)f(program.)164 1860 y(For)f(example,)h(if)g(you)f(want)h
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423 y(6)p eop
424 %%Page: 7 8
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438 (\256le)g(that)f(use)164 849 y(most)c(of)g(these)h(new)g(commands.)18
439 b(See)12 b(the)h Fc(examples)f Fh(directory)m(.)164 996
440 y Fb(9.1)59 b(New)15 b(Step)g(1)g(Commands)164 1090 y
441 Fh(SCREENSIZE)f(120)164 1150 y(Usually)g(you)g(should)g(not)g(need)g
442 (to)g(change)g(this)g(value,)h(it)f(alters)g(the)g(screening)g(used)g
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444 (used)g(by)g(default.)25 b(On)15 b(most)f(300dpi)h(black)f(and)h(white)
445 164 1271 y(printers)f(this)h(gives)g(much)f(smoother)g(greys)h(than)f
446 (the)h(default)f(used)h(in)g(earlier)f(versions)164 1331
447 y(of)e(ALSCRIPT)l(.)164 1391 y(PIR)p 245 1391 15 2 v
448 17 w(SA)-6 b(VE)13 b(\256lename)164 1451 y(W)n(ill)h(cause)g(the)g
449 (block)g(\256le)g(to)f(be)h(saved)h(into)f(the)f(\256le)h
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451 1511 y(can)13 b(be)f(useful)g(for)g(moving)f(block)i(\256le)f
452 (alignments)g(to)g(other)g(programs.)164 1572 y(MSF)p
453 267 1572 V 18 w(SA)-6 b(VE)12 b(\256lename)164 1632 y(W)n(ill)17
454 b(cause)i(the)e(block)h(\256le)f(to)h(be)f(saved)i(into)e(the)g(\256le)
455 h(\252\256lename\272)f(in)h(something)f(that)164 1692
456 y(approximates)12 b(GCG)g(.msf)h(format.)k Fc(W)-5 b(arning!)19
457 b(This)12 b(has)h(not)f(been)g(fully)g(tested.)164 1752
458 y Fh(NUMBER)p 379 1752 V 19 w(COLOUR)h(4)164 1812 y(Sets)20
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465 b(AGE)164 2053 y(If)13 b(this)g(is)h(set,)g(ALSCRIPT)g(assumes)h
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473 w(ON)p 461 2294 V 18 w(FIRST)p 615 2294 V 17 w(LINE)164
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480 %%Page: 8 9
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487 w(BOX)g(x)g(y)h(x1)f(y1)164 556 y(De\256nes)h(the)g(bounding)f(box)g
488 (for)g(the)g(\256gure.)19 b(This)13 b(is)g(set)h(in)e(points)h(\(1/72)f
489 (inch\).)18 b(NOTE:)164 616 y(In)12 b(version)g(2.0)h(this)f(was)h(a)g
490 (STEP)f(2)h(Command.)164 677 y(BACKGROUND)p 518 677 V
491 18 w(REGION)g(x)f(y)h(x1)f(y1)164 737 y(De\256nes)h(the)g(region)f(to)h
492 (colour)f(as)i(background)e(-)h(the)f(default)h(is)g(set)g(up)g(for)f
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494 (with)g(this.)25 b(V)-6 b(alues)15 b(are)g(points)f(\(1/72)g(inch\).)24
495 b(NOTE:)15 b(In)164 857 y(version)d(2.0)h(this)f(was)h(a)g(STEP)f(2)h
496 (Command.)164 1004 y Fb(9.2)59 b(New)15 b(Step)g(2)g(Commands)164
497 1098 y Fh(COLOUR)p 371 1098 V 19 w(TEXT)p 516 1098 V
498 19 w(REGION)d(x)h(y)f(x1)g(y1)h(colour)164 1158 y(Sets)8
499 b(the)g(colour)g(for)g(TEXT)g(command)g(output.)14 b(Similar)8
500 b(syntax)g(to)g(COLOUR)p 1568 1158 V 17 w(REGION,)164
501 1218 y(FONT)p 297 1218 V 18 w(REGION)13 b(etc.)164 1279
502 y(COLOUR)p 371 1279 V 19 w(LINE)p 503 1279 V 18 w(REGION)g(x)f(y)g(x1)h
503 (y1)f(colour)164 1339 y(Set)g(the)g(colour)g(for)g(LINEs)h(in)f(a)h
504 (region.)164 1399 y(CALCONS)g(x)f(y)h(x1)f(y1)164 1459
505 y(Calculate)21 b(conservation)f(values)h(according)f(to)g(Zvelebil)h
506 Fc(et)g(al.)43 b Fh(for)19 b(the)i(designated)164 1519
507 y(region.)d(\(See)12 b(Livingstone)g(&)g(Barton)g(1993)g(for)g(details)
508 g(and)h(further)e(refs\))164 1579 y(MASK)h(CONSER)l(V)-6
509 b(A)g(TION)13 b(cutof)o(f)164 1640 y(If)j(CONSCAL)h(has)g(been)g(used,)
510 h(then)f(mask)f(residues)h(according)f(to)h(the)f(conservation)164
511 1700 y(cutof)o(f.)164 1760 y(e.g.)28 b(MASK)15 b(CONSER)l(V)-6
512 b(A)g(TION)16 b(10)f(would)g(mask)g(all)g(identities,)i(MASK)e(CONSER-)
513 164 1820 y(V)-6 b(A)g(TION)14 b(6)h(would)f(mask)h(reasonably)f
514 (conserved)g(positions.)25 b(See)14 b(examples)h(for)f(more)164
515 1880 y(on)e(this)h(command.)164 1941 y(HELIX)g(x1)f(y)g(x2)164
516 2001 y(Draw)g(a)h(helix)f(from)f(x1)h(to)g(x2)h(of)f(sequence)h(y)m(.)
517 164 2061 y(STRAND)g(x1)f(y)g(x2)164 2121 y(Draw)g(a)h(strand)f(from)f
518 (x1)h(to)h(x2)f(of)g(sequence)h(y)m(.)164 2181 y(COIL)g(x1)f(y)g(x2)164
519 2242 y(Draw)g(a)h(coil)f(\(horizontal)f(line\))h(from)f(x1)h(to)g(x2)h
520 (of)f(sequence)h(y)m(.)164 2302 y(RELA)-6 b(TIVE)p 403
521 2302 V 20 w(T)o(O)13 b(<seqnum>)f(<startnum>)164 2362
522 y(Set)20 b(reference)f(numbers)h(to)g(work)f(relative)h(to)g(sequence)g
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524 (subsequent)i(commands,)f(ALSCRIPT)g(will)g(translate)g(your)f(x)h
525 (values)164 2482 y(into)f(absolute)g(position)f(values)i(in)f(the)f
526 (alignment.)20 b(This)14 b(is)f Fc(extr)n(emely)h Fh(useful)f(since)g
527 (you)961 2607 y(8)p eop
528 %%Page: 9 10
529 9 9 bop 164 315 a Fh(can)13 b(annotate)g(your)g(alignment)f(using)i
530 (your)e(favourite)g(sequences)i(as)g(a)g(reference)e(point.)164
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533 y(<startnum>)c(is)h(optional.)16 b(If)8 b(present,)i(it)e(speci\256es)h
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535 496 y(sequence)14 b(is.)24 b(For)13 b(example,)h(you)g(may)g(be)g
536 (showing)f(residues)h(200-500)f(of)h(a)g(sequence,)164
537 556 y(so)f(<startnum>)g(would)f(be)i(200)e(rather)h(than)f(the)h
538 (default)g(of)f(1.)20 b Fc(W)-5 b(arning)14 b(-)f(this)g(is)g(a)g(very)
539 164 616 y(new)g(featur)n(e)f(and)h(bounds)f(checking)g(is)h(not)f
540 (fully)g(enabled)g(for)h(it)p Fh(.)164 677 y(Y)-5 b(ou)8
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542 b(several)g(times)g(in)g(the)g(command)g(\256le)g(to)g(annotate)g(dif)o
543 (f)o(erent)164 737 y(sequences.)19 b(RELA)-6 b(TIVE)p
544 635 737 V 20 w(T)o(O)13 b(0)g(resets)f(to)h(the)f(\252normal\272)g
545 (alignment)f(numbering.)164 884 y Fb(9.3)59 b(New)15
546 b(special)f(TEXT)h(commands)164 978 y Fh(Some)e(special)i(TEXT)g
547 (commands)e(have)h(been)g(added)g(to)g(allow)f(drawing)g(of)h
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551 (pre\256xed)g(by)g(an)h(@)f(symbol.)164 1158 y(e.g.)19
552 b(TEXT)14 b(3)e(6)g(\252@fuparrow\272)164 1218 y(will)g(draw)g(a)h
553 (\256lled)e(up)i(arrow)e(at)i(position)f(3,6.)164 1279
554 y(The)h(alternative)f(text)g(commands)g(are:)164 1339
555 y(@leftarrow)f(-)h(an)g(open)h(left)f(pointing)f(arrow)m(.)164
556 1399 y(@\257eftarrow)g(-)h(a)g(\256lled)g(left)g(pointing)g(arrow)m(.)
557 164 1459 y(@uparrow)f(-)h(an)h(open)f(up)g(pointing)g(arrow)m(.)164
558 1519 y(@fuparrow)f(-)h(a)g(\256lled)g(up)h(pointing)e(arrow)m(.)164
559 1580 y(@downarrow)g(-)h(an)h(open)f(down)g(pointing)g(arrow)m(.)164
560 1640 y(@fdownarrow)f(-)h(a)g(\256lled)g(down)g(pointing)g(arrow)m(.)164
561 1700 y(@circle)g(-)g(an)g(open)h(circle.)164 1760 y(@fcircle)f(-)g(a)g
562 (\256lled)g(circle.)164 1820 y(I)g(plan)g(to)g(make)h(this)f(option)g
563 (more)g(\257exible)g(in)g(the)g(near)g(future.)164 1990
564 y Fg(10)71 b(Running)17 b(ALSCRIPT)164 2116 y Fb(10.1)59
565 b(Basic)14 b(Use)164 2210 y Fh(I)h(recommend)g(you)g(read)g(through)g
566 (this)g(section,)i(then)e(scan)h(the)g(commands)f(in)g(Section)164
567 2270 y(15.1)25 b(to)12 b(get)h(a)f(feel)g(for)g(what)g(ALSCRIPT)h(can)f
568 (do.)164 2330 y(See)i(Section)g(15.8for)g(alternative)f(methods)h(of)g
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570 y(the)9 b(interactive)f(method)h(is)g(described.)17 b(The)10
571 b(QUICK)f(ST)l(AR)m(T)h(method)e(shown)i(in)e(Section)961
572 2607 y(9)p eop
573 %%Page: 10 11
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575 (sequence)g(alignment)e(quickly)h(using)g(standard)g(pointsize)164
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577 (with)g(AMPS)g(block)g(\256le)g(format)f(multiple)h(alignments.)164
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580 h(be)f(translated)g(to)h(AMPS)f(block)g(\256le)g(format.)164
581 616 y(T)m(o)18 b(translate)g(a)g(GCG)g(.MSF)g(\256le:)29
582 b(T)m(ype:)g(msf2blc.)34 b(T)m(o)18 b(translate)g(a)g(CLUST)l(AL)h(PIR)
583 164 677 y(format)11 b(\256le,)i(or)f(any)g(PIR)g(format)f(\256le:)18
584 b(clus2blc.)164 737 y(Both)10 b(programs)g(prompt)f(for)g(the)h(name)h
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602 b(the)h(block)f(file)h(to)f(format)164 1670 y(OUTPUT_FILE)59
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624 y(10)p eop
625 %%Page: 11 12
626 11 11 bop 164 315 a Fh(The)18 b(simple)g(example)g(outlined)f(above)h
627 (can)g(be)g(modi\256ed)f(with)g(a)h(variety)f(of)h(STEP)g(2)164
628 376 y(commands.)164 436 y(for)12 b(example)g(\256le)g(example2.als:)164
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652 (20)164 1995 y(FONT_CHARS)f(C)h(ALL)f(3)418 b(#Use)30
653 b(font)f(3)h(\(BOLD)f(Helvetica\))g(for)h(C)f(characters)164
654 2055 y(ID_FONT)g(ALL)h(1)567 b(#set)30 b(identifiers)e(in)i(font)g(1)
655 164 2229 y Fh(There)9 b(are)g(many)g(possible)g(ways)g(of)g(combining)f
656 (these)h(commands)g(and)g(the)g(others)g(shown)164 2289
657 y(in)j(Section)f(15.1)h(.)19 b(In)11 b(general,)h(if)g(you)g(apply)f
658 (multiple)h(commands)f(to)h(the)g(same)h(residue,)164
659 2350 y(the)j(ef)o(fect)g(of)g(the)g(last)g(applied)g(command)g
660 (persists)g(where)g(there)g(would)g(otherwise)g(be)164
661 2410 y(a)g(con\257ict.)28 b(Thus)17 b(the)e(intersection)h(of)f(two)h
662 (overlapping)e(SHADed)i(regions)f(would)h(be)164 2470
663 y(shaded)d(according)g(to)g(the)g(second)g(SHADE)h(command,)f(not)g
664 (some)g(mixture)f(of)h(the)g(two.)949 2607 y(1)n(1)p
665 eop
666 %%Page: 12 13
667 12 12 bop 164 315 a Fh(Similarly)9 b(for)g(FONT)h(commands.)18
668 b(BOX)10 b(and)g(SURROUND)h(commands)f(behave)g(in)g(the)164
669 376 y(opposite)h(sense,)i(all)e(BOXing)g(and)g(SURROUNDing)g(persists)g
670 (regardless)h(of)e(how)h(many)164 436 y(commands)k(you)h(issue.)28
671 b(This)16 b(makes)f(it)h(possible)f(for)g(example,)h(to)g(SURROUND)f
672 (two)164 496 y(dif)o(ferent)c(sets)i(of)f(residues)h(as)g(follows:)164
673 648 y Fd(SURROUND_CHARS)28 b(DE)i(ALL)164 708 y(SURROUND_CHARS)e(DEHKR)
674 i(ALL)164 860 y Fh(This)13 b(would)g(result)f(in)h(D)f(and)h(E)g
675 (characters)g(being)f(partitioned)g(from)f(the)i(rest)g(as)g(well)f(as)
676 164 920 y(D)g(E)h(H)g(K)f(R)h(characters)f(\(see)h(Example)f(output\).)
677 164 1064 y Fb(10.2)59 b(Mor)o(e)15 b(complex)e(effects)h(-)g(T)-5
678 b(ext)14 b(Lines,)h(and)g(Masks)164 1158 y Fh(T)m(ext,)f(lines)g(and)g
679 (masking)f(are)h(meant)f(to)g(be)h(used)g(to)f(annotate)h(the)f
680 (multiple)g(alignment.)164 1218 y(The)20 b(TEXT)i(command)d(allows)h
681 (any)g(piece)g(of)g(text)g(to)g(be)g(located)g(anywhere)f(on)h(the)164
682 1279 y(alignment.)33 b(Clearly)m(,)19 b(however)e(it)g(makes)h(little)f
683 (sense)i(to)e(superimpose)h(the)f(text)g(over)164 1339
684 y(the)c(alignment)e(though)i(this)f(can)h(be)g(done!)18
685 b(Accordingly)m(,)12 b(you)g(must)h(\256rst)f(make)g(a)h(space)164
686 1399 y(to)i(put)h(the)f(text)g(in.)28 b(Usually)m(,)17
687 b(this)e(will)g(be)h(a)g(few)f(lines)h(below)f(the)h(multiple)e
688 (sequence)164 1459 y(alignment,)e(but)f(you)h(may)g(want)g(to)f(add)h
689 (text)g(at)g(the)g(top,)g(or)g(somewhere)f(in)h(between)g(two)164
690 1519 y(sequences.)25 b(Y)-5 b(ou)15 b(can)f(make)h(space)g(in)f(two)g
691 (ways.)25 b(Either)14 b(by)h(editing)e(the)i(block-\256le)e(to)164
692 1579 y(introduce)f("dummy")g(sequences)i(at)f(the)f(locations)h(you)g
693 (want,)g(or)f(by)g(making)h(use)g(of)f(the)164 1640 y(ADD)p
694 275 1640 15 2 v 18 w(SEQ)g(command.)164 1700 y(The)h(ADD)p
695 365 1700 V 18 w(SEQ)f(command)g(has)h(two)f(ar)o(guments,)h(the)f
696 (sequence)h(after)f(which)g(you)g(want)164 1760 y(further)c(sequences)i
697 (to)g(be)f(added,)i(and)e(how)g(many)g(blank)h(sequences)g(you)f(need.)
698 18 b(Thus,)11 b(we)164 1820 y(can)h(reserve)h(space)g(for)e(5)h(lines)h
699 (of)f(text)g(underneath)g(a)g(10)g(sequence)h(multiple)f(alignment)164
700 1880 y(with)g(the)g(following)f(command.)164 1941 y(ADD)p
701 275 1941 V 18 w(SEQ)h(10)h(5)164 2001 y(we)g(can)f(then)g(put)g(text)h
702 (below)f(the)g(alignment)g(at)g(the)h(20th)f(residue.)164
703 2061 y(TEXT)i(20)e(13)g("Active)h(Site)f(His")164 2121
704 y(or)g(any)g(other)g(position.)164 2181 y(Similarly)m(,)f(we)i(could)f
705 (draw)g(a)g(vertical)g(line)g(to)h(point)e(out)i(which)f(residue)g(we)h
706 (mean)164 2242 y(LINE)g(LEFT)g(20)g(13)f(1)n(1)164 2302
707 y(And)g(change)h(the)f(font)g(of)g(the)g(text)g(to)g(number)g(7)g
708 (\(whatever)g(that)g(has)h(been)g(set)f(to\):)164 2362
709 y(FONT)p 297 2362 V 18 w(RESIDUE)h(20)f(13)g(7)164 2422
710 y(Y)-5 b(ou)16 b(can)h(have)f(multiple)g(ADD)p 751 2422
711 V 18 w(SEQ)g(commands,)i(but)e(they)h(must)f(occur)g(in)g(sequence)164
712 2482 y(order)m(.)i(Thus:)949 2607 y(12)p eop
713 %%Page: 13 14
714 13 13 bop 164 315 a Fd(ADD_SEQ)29 b(0)h(5)164 376 y(ADD_SEQ)f(5)h(12)
715 164 480 y Fh(is)13 b(legal.)18 b(But)164 575 y Fd(ADD_SEQ)29
716 b(5)h(12)164 635 y(ADD_SEQ)f(0)h(5)164 730 y Fh(Is)9
717 b(NOT!!)17 b(NO)9 b(CHECKING)h(IS)e(performed)g(by)i(the)f(program)f
718 (for)g(this)i(error)e(-)h(so)g(beware!)164 790 y(Note)15
719 b(that)g(add)p 441 790 15 2 v 18 w(seq)h(commands)f(refer)f(to)i(the)f
720 (actual)g(sequence)h(number)f(as)g(implied)g(by)164 850
721 y(the)j(block)f(\256le,)i(not)f(the)g(number)f(after)g(applying)g(the)h
722 (add)p 1252 850 V 17 w(seq)h(command.)34 b(Thus,)20 b(for)164
723 910 y(a)d(four)e(sequence)j(block)e(\256le,)i(if)e(you)g(want)h(to)f
724 (add)h(space)g(for)f(three)g(sequences)i(before)164 970
725 y(sequence)13 b(1)f(and)h(two)f(sequences)h(after)f(sequence)h(3,)g
726 (the)f(commands)g(would)g(be:)164 1075 y Fd(ADD_SEQ)29
727 b(0)h(3)164 1135 y(ADD_SEQ)f(3)h(2)164 1240 y Fh(T)m(ext)13
728 b(added)g(with)g(the)g(TEXT)h(command)f(will)g(not)g(be)g(split)g
729 (across)h(page)f(breaks,)h(so)f(you)164 1300 y(may)i(in)g(some)h
730 (circumstances)g(need)f(to)g(\256ddle)g(a)h(little)f(with)g(the)g
731 (location/pointsize)g(for)164 1360 y(the)d(text)g(to)h(get)f(the)g
732 (desired)h(result.)164 1420 y(Masking)g(is)g(a)f(technique)h(for)e
733 (drawing)h(irregular)f(shaped)i(outlines,)g(or)f(shaded)h(regions)f(-)
734 164 1480 y(this)e(should)g(not)g(be)g(confused)g(with)f(the)h(MASK)g
735 (family)f(of)h(commands)g(described)g(below)m(.)164 1541
736 y(For)18 b(example)h(a)h(histogram)e(can)h(be)h(added)f(to)g(the)g
737 (bottom)f(of)h(an)g(alignment)f(by)h(\256rst)164 1601
738 y(de\256ning)11 b(some)g(dummy)g(sequences)i(in)e(the)g(block-\256le)g
739 (that)g(have)h(letters)f(building)g(up)g(the)164 1661
740 y(shape)f(of)f(the)h(histogram,)g(then)f(using)h(the)f(SURROUND)p
741 1191 1661 V 18 w(CHARS)h(or)f(SHADE)p 1602 1661 V 18
742 w(CHARS)164 1721 y(commands)f(together)g(with)g(the)g(SUB)p
743 826 1721 V 18 w(CHARS)g(command)g(to)h(produce)e(the)i(desired)f(ef)o
744 (fect.)164 1781 y(An)g(example)g(of)g(this)g(operation)g(being)g(used)g
745 (to)g(show)g(fr)o(equencies)g(of)g(secondary)g(str)o(ucture)164
746 1842 y(predictions)k(is)g(shown)h(in)f(example1.als)h(and)g(in)f(the)g
747 (Protein)f(Engineering)h(paper)m(.)164 2010 y Fg(1)l(1)71
748 b(Using)18 b(Colour)164 2121 y Fh(V)-6 b(ersion)12 b(1.4)h(includes)f
749 (commands)g(to)g(allow)g(the)g(independent)g(colouring)f(of)h
750 (characters,)164 2181 y(or)i(their)g(backgrounds.)24
751 b(Colours)14 b(are)g(de\256ned)h(in)f(a)g(similar)g(manner)g(to)g
752 (fonts)h(using)f(the)164 2242 y(DEFINE)p 344 2242 V 18
753 w(COLOUR)f(command)f(\(American)g(spelling)g(also)h(allowed\).)k(For)12
754 b(example:)164 2302 y(DEFINE)p 344 2302 V 18 w(COLOUR)h(7)g(1)f(0)g(0)
755 164 2362 y(de\256nes)21 b(colour)f(number)h(7)g(to)f(be)h(red)g(-)g
756 (see)g(Section)g(15.1)42 b(for)20 b(full)g(details)h(of)g(this)164
757 2422 y(command.)26 b(Colours)16 b(99)f(and)g(100)g(are)g(pre-de\256ned)
758 f(to)h(white)g(and)h(black.)27 b(ALSCRIPT)164 2482 y(assumes)13
759 b(the)g(paper)f(colour)g(is)g(white.)949 2607 y(13)p
760 eop
761 %%Page: 14 15
762 14 14 bop 164 315 a Fh(The)13 b(command)f(to)g(colour)g(the)g(text)g
763 (of)g(a)h(character)f(or)g(text)g(string)g(is:)164 376
764 y(CCOL)p 299 376 15 2 v 19 w(CHARS)164 436 y(the)g(command)g(to)g
765 (colour)g(the)g(background)g(of)g(a)h(character)f(is)164
766 496 y(SCOL)p 294 496 V 18 w(CHARS)164 556 y(both)g(have)g(similar)g
767 (syntax)h(to)f(the)g(FONT)p 922 556 V 18 w(CHARS)h(command.)164
768 616 y(COLOUR)p 371 616 V 19 w(REGION)7 b(and)g(COLOUR)p
769 868 616 V 19 w(RES)g(have)g(similar)g(syntax)g(to)g(SHADE)p
770 1581 616 V 20 w(REGION)164 677 y(and)12 b(SHADE)p 417
771 677 V 18 w(RES.)164 737 y(An)g(example)h(command)e(\256le)i(that)f
772 (uses)h(colour)f(is)g(shown)h(in)f(example3.als.)164
773 906 y Fg(12)71 b(The)18 b(MASK)f(command)g(family)164
774 1018 y Fh(The)f(idea)f(behind)g(the)h(MASK)f(command)g(is)g(to)h(build)
775 f(up)g(a)g(set)h(of)f(character)g(positions)164 1078
776 y(that)c(will)g(subsequently)g(be)h(boxed,)f(shaded,)i(set)e(in)g(a)h
777 (particular)e(font,)h(etc.)18 b(For)11 b(example,)164
778 1138 y(lets)h(say)h(we)f(want)g(to)g(box)f(the)h(most)g(frequently)f
779 (occuring)h(character)f(at)h(each)h(position)e(in)164
780 1198 y(an)h(alignment.)164 1259 y(The)h(command)164 1319
781 y(mask)g(SETUP)164 1379 y(tells)f(ALSCRIPT)h(to)f(prepare)g(a)h(mask.)
782 164 1439 y(mask)g(FRE)f(ALL)164 1499 y(speci\256es)h(that)f(the)h(most)
783 f(frequently)f(occuring)h(character)g(at)g(each)h(position)f(in)g(the)h
784 (align-)164 1559 y(ment)d(will)g(be)h(masked.)18 b(This)11
785 b(command)f(can)g(be)h(restricted)f(to)g(a)h(region)e(of)h(the)h
786 (alignment)164 1620 y(using:)21 b(mask)14 b(FRE)h(sx)f(sy)h(ex)f(ey)m
787 (,)h(where)f(sx)g(etc)g(de\256ne)g(the)g(region)g(in)g(the)g(same)g
788 (way)g(as)164 1680 y(for)e(font)p 319 1680 V 17 w(region)f(and)i(other)
789 f(commands.)164 1740 y(mask)h(BOX)f(ALL)164 1800 y(T)m(ells)d(ALSCRIPT)
790 g(to)g(create)f(the)h(boxing)f(lines)h(that)g(will)f(separate)h(the)g
791 (masked)g(characters)164 1860 y(from)i(non-masked)h(characters)h(-)f
792 (this)h(command)f(may)g(also)h(be)g(restricted)e(to)i(a)g(region)e(of)
793 164 1921 y(the)h(alignment.)164 1981 y(The)h(mask)f(can)h(be)g(reset)f
794 (for)g(re-use)g(using)g(the)g(command:)164 2041 y(mask)h(RESET)164
795 2101 y(T)m(wo)f(further)g(commands)g(de\256ne)h(which)f(characters)h
796 (can)f(be)h(used)g(when)g(calculating)f(the)164 2161
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798 (acids)h(to)f(be)h(excluded)g(from)e(the)164 2222 y(calculation)f(to)g
799 (avoid)g(unwanted)g(boxing.)164 2282 y(mask)h(LEGAL)g("A)-6
800 b(VLI")164 2342 y(de\256nes)11 b(the)g(A)-6 b(VL)10 b(and)h(I)f(as)i
801 (the)e(only)h(characters)f(that)h(will)f(be)h(used)g(when)g
802 (calculating)f(the)164 2402 y(mask.)164 2462 y(mask)j(ILLEGAL)g(".-)p
803 556 2462 V 19 w(")949 2607 y(14)p eop
804 %%Page: 15 16
805 15 15 bop 164 315 a Fh(de\256nes)18 b(.-)h(and)p 464
806 315 15 2 v 54 w(as)g(characters)f(that)g(will)g(not)g(be)g(used)h(when)
807 f(calculating)g(the)g(mask.)164 376 y(NOTE:)d(the)f(blank)h(character)f
808 (")g(")h(cannot)g(be)f(de\256ned)g(in)g(this)h(way)m(.)24
809 b(T)m(o)15 b(avoid)f(boxing)g(")164 436 y(")g(characters)f(substitute)h
810 (blanks)f(for)g(something)g(else)g(\(using)g(SUB)p 1382
811 436 V 18 w(CHARS\),)h(calculate)164 496 y(the)e(mask,)h(then)g
812 (substitute)f(back.)164 643 y Fb(12.1)59 b(Summary)15
813 b(of)f(mask)i(commands)164 737 y Fh(mask)d(SETUP)f(#)h(Prepares)f(for)f
814 (masking)164 797 y(mask)19 b(LEGAL)h Fe(<)p Fh(qstring)p
815 Fe(>)e Fh(#)g(de\256nes)h(characters)g(to)f(include)g(in)h(ID)f(or)g
816 (FRE)h(calcs)g(-)164 857 y(optional.)164 917 y(mask)c(ILLEGAL)g
817 Fe(<)p Fh(qstring)p Fe(>)f Fh(#)g(de\256nes)h(characters)f(to)g
818 (exclude)h(in)f(ID)g(or)g(FRE)g(calcs)h(-)164 978 y(optional.)164
819 1038 y(mask)d(ID)f(ALL)i(N)f(#)f(Calculates)i(a)f(mask)f(that)h
820 (\257ags)g(the)f(character)h(that)f(occurs)h(at)g(least)g(N)164
821 1098 y(times)g(at)f(a)h(position.)18 b(The)12 b(word)f(ALL)i(can)f(be)f
822 (substituted)h(by)g(four)e(numbers)i(that)f(de\256ne)164
823 1158 y(a)i(region)e(of)h(the)h(alignment.)164 1218 y(mask)e(FRE)h(ALL)g
824 (#)f(calculates)h(a)g(mask)f(that)g(\257ags)g(the)h(most)f(frequently)f
825 (occuring)g(amino)164 1279 y(acid)i(at)h(each)f(position.)18
826 b(ALL)13 b(may)g(be)f(replaced)g(by)g(four)g(numbers)g(de\256ning)f(a)i
827 (region)e(of)164 1339 y(the)h(alignment.)164 1399 y(Multiple)c(mask)h
828 (FRE)f(or)g(mask)h(ID)f(commands)g(may)g(be)h(applied,)g(using)g(dif)o
829 (ferent)e(LEGAL)164 1459 y(and)i(ILLEGAL)i(character)e(de\256nitions.)
830 17 b(In)9 b(this)h(way)f(more)g(complex)g(ef)o(fects)g(can)h(be)g
831 (built)164 1519 y(up.)164 1579 y(The)h(mask)g(command)g(also)g(allows)g
832 (characters)g(that)f(are)h(identical)f(to)h(one)g(sequence)g(to)g(be)
833 164 1640 y(masked.)164 1700 y(mask)i(AGREE)g(ALL)g(N)164
834 1760 y(will)e(mask)h(all)f(positions)h(that)f(are)h(identical)f(to)h
835 (the)f(Nth)h(sequence.)18 b(Thus,)13 b(for)e(sequences)164
836 1820 y(that)g(are)g(very)g(similar)g(to)g(a)h(newly)f(sequenced)h
837 (sequence,)g(all)g(characters)f(identical)g(to)g(the)164
838 1880 y(new)h(sequence)h(can)g(be)g(boxed)f(or)g(shaded,)h(or)f(set)h
839 (in)f(a)g(dif)o(ferent)f(font)h(or)g(colour)g(etc...)164
840 1941 y(mask)h(NOT)f(ALL)164 2001 y(allows)18 b(the)h(mask)f(to)h(be)f
841 (inverted.)36 b(Thus,)21 b(all)d(positions)g(that)g(are)g(NOT)h(in)f
842 (the)h(mask)164 2061 y(now)d(form)e(the)i(mask.)29 b(So,)17
843 b(having)f(done)g(a)g(mask)g(AGREE,)h(a)f(mask)g(NOT)h(will)e(allow)164
844 2121 y(the)h(positions)g(that)g(are)g(not)g(identical)g(to)g(the)g
845 (selected)g(sequence)h(to)f(be)g(highlighted)f(or)164
846 2181 y(substituted.)164 2242 y(mask)e(SUB)f(ALL)h Fe(<)p
847 Fh(char)p Fe(>)164 2302 y Fh(substitutes)g(all)f(characters)g(in)h(the)
848 f(mask)h(with)f(the)g(character)g Fe(<)p Fh(char)p Fe(>)p
849 Fh(.)164 2362 y(mask)h(REGION)f(ALL)h(applies)g(a)g(mask)f(to)g(all)h
850 (residues)f(in)h(the)f(de\256ned)g(region.)164 2422 y(The)h(following)e
851 (ef)o(fects)h(can)h(now)f(be)h(applied)f(to)g(the)g(masked)h
852 (characters:)164 2482 y(mask)g(BOX)f(ALL)h(#)g(boxes)g(the)f(masked)g
853 (residues)h(-)f(ie)h(surrounds)f(them)g(by)g(lines.)949
854 2607 y(15)p eop
855 %%Page: 16 17
856 16 16 bop 164 315 a Fh(mask)13 b(SHADE)f(ALL)h Fe(<)p
857 Fh(grey)p Fe(>)f Fh(#)h(shades)g(the)f(masked)h(residues)f(by)h(grey)f
858 (value.)164 376 y(mask)e(FONT)g(ALL)g Fe(<)p Fh(fontnum)p
859 Fe(>)f Fh(#)g(Uses)i(font)e(fontnum)f(to)i(output)f(the)g(masked)h
860 (residues.)164 436 y(mask)j(INVERSE)f(ALL)i(#)e(Inverts)g(the)g(masked)
861 h(characters)f(-)g(ie)h(outputs)f(them)g(in)g(white.)164
862 496 y(mask)21 b(CCOL)g(ALL)g Fe(<)p Fh(colnum)p Fe(>)f
863 Fh(#)h(outputs)f(the)g(masked)h(characters)g(in)f(the)g(de\256ned)164
864 556 y(colour)m(.)164 616 y(mask)11 b(SCOL)g(ALL)h Fe(<)p
865 Fh(colnum)p Fe(>)f Fh(#)f(outputs)h(the)g(backgrounds)g(of)f(the)h
866 (masked)g(characters)164 677 y(in)h(the)h(de\256ned)f(colour)m(.)164
867 737 y(In)17 b(all)g(commands,)i(the)e(word)f(ALL)j(can)e(be)g(replaced)
868 g(by)g(four)g(numbers)f(de\256ning)h(the)164 797 y(region)12
869 b(to)g(which)g(the)g(command)g(is)h(applied.)164 857
870 y(mask)g(RESET)g(#)g(resets)f(the)h(entire)f(mask)g(for)g(re-use)164
871 1027 y Fg(13)71 b(Printing)17 b(ALSCRIPT)g(Files)164
872 1138 y Fh(ALSCRIPT)i(produces)f(\256les)h(in)f(PostScript)g(which)g
873 (may)h(be)f(printed)g(on)g(a)h(PostScript)164 1198 y(printer)14
874 b(\(e.g.)25 b(an)15 b(Apple)g(LaserW)n(riter\).)24 b(If)14
875 b(you)h(don')o(t)f(have)h(a)g(PostScript)e(printer)n(,)i(then)164
876 1259 y(you)9 b(may)f(still)h(be)g(able)g(to)g(use)g(ALSCRIPT)g(if)g
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878 1319 y(This)j(is)f(a)g(free)g(package)g(that)g(interprets)g(PostScript)
879 f(commands)h(and)g(can)g(produce)g(output)164 1379 y(on)g(a)g(lar)o(ge)
880 g(number)f(of)h(dif)o(ferent)f(types)h(of)g(printer)m(.)16
881 b(GhostScript)10 b(runs)g(on)g(most)g(hardware)164 1439
882 y(types)e(\(including)g(PCs\))g(and)g(can)g(also)g(display)g(output)g
883 (to)g(the)g(screen.)17 b(The)8 b(package)g(can)g(be)164
884 1499 y(obtained)i(from)g(many)h(dif)o(ferent)e(sites)i(on)g(the)g
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886 1559 y(The)k(actual)f(command)g(you)g(need)h(to)f(type)g(to)h(send)f(a)
887 h(PostScript)e(\256le)i(to)f(the)g(printer)f(will)164
888 1620 y(depend)g(on)h(your)e(system.)19 b(Consult)13 b(your)e(system)i
889 (manager)f(for)g(help.)164 1680 y(Be)e(warned,)g(ALSCRIPT)f(can)h
890 (create)f(extremely)g(lar)o(ge)g(PostScript)f(\256les)h(if)g(lots)h(of)
891 f(boxing)164 1740 y(and)k(shading)g(is)h(done)f(on)g(big)g(alignments.)
892 20 b(On)13 b(older)g(printers)f(such)i(output)f(may)g(take)g(a)164
893 1800 y(long)f(time)g(to)g(process.)164 1970 y Fg(14)71
894 b(Conclusion)164 2081 y Fh(ALSCRIPT)11 b(provides)f(a)h(powerful)f(set)
895 h(of)f(formatting)g(and)g(editing)g(commands)h(speci\256c-)164
896 2141 y(ally)h(tailored)g(for)g(multiple)f(sequence)i(alignments.)19
897 b(It)12 b(is)h(best)f(used)h(in)g(conjunction)e(with)164
898 2202 y(a)16 b(PostScript)f(previewer)h(such)g(as)h(Sun')m(s)f(PageV)m
899 (iew)f(or)h(GhostV)m(iew)g(since)h(this)f(allows)164
900 2262 y(the)g(ef)o(fect)g(of)f(changing)h(a)g(command)g(to)g(be)g(seen)h
901 (quickly)m(.)28 b(In)16 b(the)g(absence)h(of)e(such)i(a)164
902 2322 y(tool,)h(simpler)e(ef)o(fects)h(can)g(be)g(tested)g(out)g
903 (without)f(destroying)g(too)h(many)f(trees)h(in)g(the)164
904 2382 y(Laser)c(Printer!)949 2607 y(16)p eop
905 %%Page: 17 18
906 17 17 bop 164 315 a Fh(Like)12 b(most)f(programs,)g(ALSCRIPT)g(is)h
907 (evolving)f(as)g(I)g(\256nd)g(new)g(problems)g(to)g(display)m(,)h(so)
908 164 376 y(if)g(you)g(have)h(any)f(suggestions)h(-)f(I)g(shall)g
909 (endeavour)g(to)h(include)f(them)g(in)g(a)h(later)f(version.)164
910 545 y Fg(15)71 b(Appendices)164 671 y Fb(15.1)59 b(ALSCRIPT)16
911 b(Command)e(Summary)164 765 y Fh(W)-6 b(ARNING:)17 b(V)-6
912 b(ery)16 b(little)h(error)e(checking)i(is)g(performed)e(on)h(command)h
913 (input.)30 b(If)16 b(you)164 825 y(give)d(the)f(wrong)h(number)f(of)g
914 (ar)o(guments)g(to)h(a)g(command,)g(then)g(unexpected)f(things)h(may)
915 164 885 y(happen,)i(or)f(the)h(program)e(will)h(crash)h(very)f
916 (inelegantly)m(.)23 b(I)14 b(hope)h(to)f(\256x)g(this)g(in)h(the)f
917 (next)164 945 y(version)f(of)g(the)h(program,)f(in)g(the)h(meantime,)g
918 (make)f(sure)h(you)f(give)g(the)h(correct)f(number)164
919 1006 y(of)f(ar)o(guments)g(to)g(each)h(command.)164 1066
920 y(All)g(commands)h(up)f(to)h(the)f(\256rst)g(space)i(character)e(may)g
921 (be)h(entered)f(in)h(UPPER)f(or)g(lower)164 1126 y(case)19
922 b(or)e(MiXEd)i(case.)36 b(Quali\256ers)18 b(for)f(commands)h(\(e.g.)35
923 b(REL\))19 b(must)f(be)g(written)f(in)164 1186 y(UPPER)12
924 b(case.)164 1246 y(Command)g(Reference:)164 1361 y Fd(<int>)59
925 b(=)30 b(enter)f(an)h(integer)59 b(\(e.g.)29 b(240\))164
926 1421 y(<float>)g(=)h(enter)f(a)h(floating)f(point)g(number)g(\(e.g.)h
927 (0.45\))164 1481 y(<string>)f(=)h(enter)f(a)h(string)f(\(e.g.)59
928 b(ARNDql\))164 1541 y(<qstring>)29 b(=)h(enter)f(a)h(quoted)f(string)g
929 (\(e.g.)g("Active)h(Site"\))164 1601 y(<char>)119 b(=)30
930 b(enter)f(a)h(single)f(character.)164 1734 y Ff(15.1.1)50
931 b(STEP)13 b(1)g(COMMANDS)164 1828 y Fh(These)18 b(all)f(refer)f(to)h
932 (either)g(system)h(settings)f(-)g(e.g.)33 b(the)17 b(maximum)f(allowed)
933 h(sequence)164 1888 y(length,)12 b(or)g(to)f(general)h(page)g(layout)g
934 (features.)18 b(e.g.)g(the)12 b(longest)g(and)g(shortest)g(side)g(of)g
935 (the)164 1948 y(paper)g(on)g(which)h(you)f(are)g(plotting.)164
936 2081 y Ff(15.1.2)50 b(REQUIRED)13 b(STEP)g(1)g(COMMANDS)164
937 2174 y Fh(BLOCK)p 335 2174 15 2 v 19 w(FILE)f Fe(<)p
938 Fh(string)p Fe(>)164 2235 y Fh(Gives)18 b(the)g(name)g(of)f(the)h
939 (\256le)f(that)h(contains)g(the)g(multiple)f(sequence)h(alignment)f(to)
940 h(be)164 2295 y(formatted.)33 b(File)17 b(names)h(should)g(be)g(fully)e
941 (quali\256ed)h(i.e.)35 b(not)18 b(relative)f(to)g(the)h(current)164
942 2355 y(directory)m(.)k(If)13 b(no)h(block)g(\256le)f(command)h(is)g
943 (given,)h(ALSCRIPT)f(will)f(expect)h(to)g(read)g(the)164
944 2415 y(block)e(\256le)g(from)g(standard)g(input.)164
945 2475 y(OUTPUT)p 363 2475 V 18 w(FILE)h Fe(<)p Fh(string)p
946 Fe(>)949 2607 y Fh(17)p eop
947 %%Page: 18 19
948 18 18 bop 164 315 a Fh(De\256nes)14 b(the)f(output)g(\256le)g(name.)21
949 b(This)14 b(command)e(should)i(be)f(near)g(the)h(beginning)e(of)h(the)
950 164 376 y(command)f(list.)18 b(e.g.)h(OUTPUT)p 753 376
951 15 2 v 19 w(FILE)12 b(Figure1.ps)164 436 y(Y)-5 b(ou)12
952 b(MUST)h(de\256ne)f(an)h(output)f(\256le)g(unless)h(the)f(-p)g(option)g
953 (\(See)g(Section)g(15.8)g(\))g(is)h(used.)164 496 y(DEFINE)p
954 344 496 V 18 w(FONT)g Fe(<)p Fh(int)p Fe(>)e(<)p Fh(string)p
955 Fe(>)h Fh(\()p Fe(<)p Fh(int)p Fe(>)p Fh(/DEF)l(AUL)-5
956 b(T\)/\(REL)13 b Fe(<)p Fh(\257oat)p Fe(>)p Fh(\))164
957 556 y(De\256nes)g(a)f(font)g(to)g(use)h(later:)k(e.g.)164
958 658 y Fd(DEFINE_FONT)29 b(0)g(Helvetica)g(10)164 718
959 y(DEFINE_FONT)g(2)g(Times-Roman)g(2)164 820 y Fh(de\256nes)15
960 b(font)f(number)g(0)g(to)h(be)g(10)f(point)h(Helvetica,)g(and)g(font)f
961 (number)g(2)h(to)f(be)h(2)f(point)164 880 y(T)n(imes-Roman.)29
962 b(Font)16 b(0)g(is)g(always)g(used)h(as)f(the)g(default)g(font.)28
963 b(Y)-5 b(ou)16 b(MUST)g(de\256ne)g(at)164 940 y(least)d(the)f(font)g(0)
964 g(font.)164 1000 y(DEFINE)p 344 1000 V 18 w(FONT)h(3)f(T)n(imes-Roman)h
965 (DEF)l(AUL)-5 b(T)164 1061 y(sets)16 b(font)f(3)g(to)g(be)h(T)n
966 (imes-Roman)g(at)f(whatever)g(the)g(default)g(pointsize)g(is)h(as)g
967 (set)g(by)f(the)164 1121 y(POINTSIZE)d(command.)164 1181
968 y(DEFINE)p 344 1181 V 18 w(FONT)h(4)f(Helvetica)g(REL)i(0.5)164
969 1241 y(sets)f(font)f(4)g(to)g(be)h(helvetica)f(at)h(half)e(the)i
970 (default)f(pointsize.)164 1301 y(NOTE:)h(Font)f(names)h(must)f(be)g
971 (written)g(exactly)g(as)h(shown)g(in)f(Section)g(15.3)h(.)164
972 1362 y(SETUP)164 1422 y(Signals)f(the)g(end)h(of)f(the)g(STEP)h(1)f
973 (commands.)164 1554 y Ff(15.1.3)50 b(OPTIONAL)13 b(STEP)h(1)e(COMMANDS)
974 164 1648 y Fh(ADD)p 275 1648 V 18 w(SEQ)g Fe(<)p Fh(int)p
975 Fe(>)g(<)p Fh(int)p Fe(>)164 1708 y Fh(Allows)20 b(extra)f(sequence)i
976 (positions)f(to)f(be)h(created)g(in)g(an)g(existing)f(alignment.)40
977 b(This)164 1769 y(permits)11 b(additional)g(annotations)g(to)h(be)f
978 (interspaced)h(either)f(above,)h(below)m(,)g(or)f(anywhere)164
979 1829 y(in)h(the)h(middle)e(of)h(an)h(alignment.)k(For)12
980 b(example:)164 1889 y(ADD)p 275 1889 V 18 w(SEQ)g(0)h(10)164
981 1949 y(would)f(create)g(an)h(additional)f(10)g(sequences)h(-)f(all)h
982 (set)g(to)f(the)g(blank)g(character)g(before)g(the)164
983 2009 y(\256rst)g(sequence)h(in)f(the)g(block)h(\256le)f(that)g(has)h
984 (been)f(read)g(in.)164 2069 y(ADD)p 275 2069 V 18 w(SEQ)g(3)h(1)164
985 2130 y(would)f(add)g(an)h(extra)f(sequence)h(after)f(sequence)h(3.)164
986 2190 y(IMPOR)m(T)l(ANT)n(:)22 b(If)f(you)h(use)h(the)f(ADD)p
987 916 2190 V 18 w(SEQ)g(facility)f(to)h(add)g(sequences)h(anywhere)164
988 2250 y(except)d(after)e(the)i(last)g(sequence,)i(then)e(remember)e
989 (that)i(the)f(sequence)h(numbers)f(will)164 2310 y(alter)m(.)43
990 b(All)21 b(formatting)e(commands)h(that)h(follow)f(this)g(command)g
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992 (in)g(the)f(\256rst)g(example:)164 2431 y(ADD)p 275 2431
993 V 18 w(SEQ)g(0)h(10)949 2607 y(18)p eop
994 %%Page: 19 20
995 19 19 bop 164 315 a Fh(what)20 b(was)h(sequence)g(number)e(1)h(becomes)
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999 y(only)d(change)h(for)f(commands)h(AFTER)g(the)g(SETUP)g(command,)f
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1001 496 y(commands)h(refer)g(to)g(the)g(sequence)h(number)f(as)h(implied)f
1002 (by)g(the)g(block)g(\256le.)164 556 y(POINTSIZE)g Fe(<)p
1003 Fh(int)p Fe(>)164 616 y Fh(De\256nes)f(the)h(pointsize)f(to)g(be)g
1004 (used)h(to)f(scale)h(the)f(plot)g(and)g(space)h(the)g(characters.)18
1005 b(Default)164 677 y(is)13 b(10)f(point.)164 737 y(NUMBER)p
1006 379 737 V 19 w(SEQS)164 797 y(If)k(present,)i(then)e(the)g(sequence)h
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1008 b(This)17 b(is)164 857 y(useful)12 b(for)g(\256nding)f(the)i
1009 (coordinates)f(of)g(residues)g(to)h(box)f(or)g(otherwise)g(highlight.)
1010 164 917 y(LANDSCAPE)164 978 y(Speci\256es)17 b(that)f(alignments)g
1011 (will)h(be)f(plotted)h(with)f(the)g(longest)h(paper)f(axis)h
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1013 (page)h(this)f(way\).)164 1098 y(POR)m(TRAIT)164 1158
1014 y(Speci\256es)h(that)h(alignments)f(will)g(be)h(plotted)f(with)g(the)h
1015 (longest)f(paper)g(axis)h(vertical)f(\(can)164 1218 y(get)f(more)g
1016 (sequences)i(on)e(a)g(page)h(this)f(way\).)164 1279 y(IDENT)p
1017 316 1279 V 18 w(WIDTH)h Fe(<)p Fh(int)p Fe(>)164 1339
1018 y Fh(Units)f(are)h(characters.)164 1399 y(Reserves)h
1019 Fe(<)p Fh(int)p Fe(>)e Fh(characters)h(at)g(left)g(of)g(every)f(page)h
1020 (for)g(plotting)f(identi\256ers.)19 b(Note)13 b(that)164
1021 1459 y(not)c(all)f(this)h(space)h(need)f(be)g(used,)i(if)d(a)h(smaller)
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1023 1519 y(codes,)k(than)g(is)f(used)h(for)f(the)g(main)g(alignment.)164
1024 1579 y(LINE)p 280 1579 V 18 w(WIDTH)p 464 1579 V 18 w(F)l(ACT)o(OR)i
1025 Fe(<)p Fh(\257oat)p Fe(>)164 1640 y Fh(V)-6 b(alue)15
1026 b(greater)e(than)h(0)g(that)g(scales)h(the)f(default)f(line)h(width.)23
1027 b(The)15 b(linewidth)e(is)h(obtained)164 1700 y(by)e(multiplying)f(the)
1028 i(pointsize)f(by)g(this)h(factor)m(.)164 1760 y(X)p 203
1029 1760 V 18 w(SP)-5 b(ACE)p 371 1760 V 18 w(F)l(ACT)o(OR)14
1030 b Fe(<)p Fh(\257oat)p Fe(>)164 1820 y Fh(Y)p 203 1820
1031 V 18 w(SP)-5 b(ACE)p 371 1820 V 18 w(F)l(ACT)o(OR)14
1032 b Fe(<)p Fh(\257oat)p Fe(>)164 1880 y Fh(This)f(determines)f(the)h
1033 (spacing)g(between)f(adjacent)h(residues)g(in)f(the)g(X)h(and)f(Y)h
1034 (directions.)164 1941 y(The)h(spacing)g(is)f(calculated)h(as:)20
1035 b(POINTSIZE)13 b(+)h(POINTSIZE)f(*)h(X)p 1408 1941 V
1036 18 w(SP)-5 b(ACE)p 1576 1941 V 18 w(F)l(ACT)o(OR)164
1037 2001 y(or)9 b(POINTSIZE)h(+)g(POINTSIZE)g(*)g(Y)p 851
1038 2001 V 17 w(SP)-5 b(ACE)p 1018 2001 V 19 w(F)l(ACT)o(OR)11
1039 b(as)f(appropriate.)16 b(Defaults)10 b(are)164 2061 y(0.2)j(and)f(0.0)h
1040 (respectively)m(.)164 2121 y(X)p 203 2121 V 18 w(SHIFT)p
1041 360 2121 V 17 w(F)l(ACT)o(OR)h Fe(<)p Fh(\257oat)p Fe(>)164
1042 2181 y Fh(Y)p 203 2181 V 18 w(SHIFT)p 360 2181 V 17 w(F)l(ACT)o(OR)g
1043 Fe(<)p Fh(\257oat)p Fe(>)164 2242 y Fh(These)h(determine)d(the)i(shift)
1044 f(relative)g(to)h(the)f(residue)h(drawing)e(position)i(that)f(is)h
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1046 b(shift)f(is)g(calculated)h(as)g(follows)164 2362 y(\(POINTSIZE)h(+)g
1047 (POINTSIZE)g(*)g(X)p 833 2362 V 18 w(SP)-5 b(ACE)p 1001
1048 2362 V 18 w(F)l(ACT)o(OR\))15 b(*)f(X)p 1317 2362 V 18
1049 w(SHIFT)p 1474 2362 V 17 w(F)l(ACT)o(OR)h(sim-)164 2422
1050 y(ilarly)d(for)f(Y)p 391 2422 V 18 w(SHIFT)p 548 2422
1051 V 17 w(F)l(ACT)o(OR.)164 2482 y(The)i(defaults)f(are)g(0.3)h(and)f(0.0)
1052 h(respectively)m(.)949 2607 y(19)p eop
1053 %%Page: 20 21
1054 20 20 bop 164 315 a Fh(Fiddling)10 b(with)h(the)g(X)p
1055 555 315 15 2 v 18 w(SP)-5 b(ACE/SHIFT)11 b(values)h(is)f(useful)h(to)f
1056 (\256ne)g(tune)g(the)g(appearance)g(of)164 376 y(the)h(alignment.)164
1057 436 y(MAX)p 283 436 V 18 w(INPUT)p 448 436 V 18 w(LEN)h
1058 Fe(<)p Fh(int)p Fe(>)164 496 y Fh(Units)h(are)g(characters.)23
1059 b(De\256nes)14 b(the)g(maximum)f(number)g(of)g(characters)h(possible)g
1060 (in)g(the)164 556 y(input)g(line)h(length.)25 b(This)16
1061 b(must)f(be)g(greater)f(than)h(the)f(maximum)g(number)h(of)f(sequences)
1062 164 616 y(\(MAX)p 300 616 V 18 w(NSEQ\).)164 677 y(e.g.)19
1063 b(MAX)p 373 677 V 18 w(INPUT)p 538 677 V 18 w(LEN)13
1064 b(600)164 737 y(Increases)g(the)f(default)g(value)g(of)g(500)g
1065 (characters)h(to)f(600)g(characters.)164 797 y(MAX)p
1066 283 797 V 18 w(NSEQ)h Fe(<)p Fh(int)p Fe(>)164 857 y
1067 Fh(Units)d(are)h(characters.)17 b(De\256nes)11 b(the)f(maximum)g
1068 (number)f(of)h(sequences)h(that)g(may)f(be)g(read)164
1069 917 y(by)g(the)h(program.)16 b(This)11 b(parameter)f(has)h(a)g(lar)o
1070 (ge)f(default)g(\(500\).)17 b(Y)-5 b(ou)10 b(may)g(need)h(to)f(reduce)
1071 164 978 y(it)i(on)g(computers)g(with)g(small)h(memories.)164
1072 1038 y(MAX)p 283 1038 V 18 w(ILEN)g Fe(<)p Fh(int)p Fe(>)164
1073 1098 y Fh(Units)e(are)f(characters.)18 b(The)11 b(maximum)f(length)g
1074 (allowed)h(for)f(a)g(sequence)i(identi\256er)d(code.)164
1075 1158 y(MAX)p 283 1158 V 18 w(SEQ)p 395 1158 V 18 w(LEN)k
1076 Fe(<)p Fh(int)p Fe(>)164 1218 y Fh(De\256nes)f(the)f(maximum)g(length)g
1077 (allowed)h(for)f(a)h(sequence)g(alignment)f(-)g(this)h(may)f(need)h(to)
1078 164 1279 y(be)g(reduced)h(from)e(the)h(8000)g(default)g(value)g(on)h
1079 (smaller)f(computers.)164 1339 y(X)p 203 1339 V 18 w(OFFSET)g
1080 Fe(<)p Fh(int)p Fe(>)g Fh(Units)h(of)f(points)g(\(1/72)f(inch\).)164
1081 1399 y(De\256nes)19 b(the)f(of)o(fset)g(along)g(the)g(X-axis)g(that)g
1082 (the)h(alignments)f(will)g(be)g(shifted)g(prior)f(to)164
1083 1459 y(printing.)35 b(Fiddle)17 b(with)h(this)h(value)f(to)g(get)g(a)g
1084 (nice)h(of)o(fset)f(from)f(the)h(bottom)f(left)h(hand)164
1085 1519 y(corner)12 b(of)g(the)g(page)g(if)g(your)g(page)h(size)f(is)h
1086 (not)f(A4.)164 1579 y(Y)p 203 1579 V 18 w(OFFSET)g Fe(<)p
1087 Fh(int)p Fe(>)g Fh(Units)h(of)f(points)g(\(1/72)f(inch\).)164
1088 1640 y(As)i(for)e(X)p 341 1640 V 18 w(OFFSET)l(,)i(only)f(Y)h(axis.)164
1089 1700 y(MAX)p 283 1700 V 18 w(SIDE)f Fe(<)p Fh(int)p Fe(>)g
1090 Fh(Units)h(of)f(inches.)164 1760 y(De\256nes)h(the)f(length)g(of)g(the)
1091 g(longest)h(side)f(of)g(the)h(printer)e(page.)164 1820
1092 y(MIN)p 264 1820 V 18 w(SIDE)h Fe(<)p Fh(int)p Fe(>)g
1093 Fh(Units)g(of)g(inches.)164 1880 y(De\256nes)h(the)f(length)g(of)g(the)
1094 g(shortest)h(side)f(of)g(the)h(printer)e(page.)164 1941
1095 y(VER)m(TICAL)p 409 1941 V 19 w(SP)-5 b(ACING)12 b Fe(<)p
1096 Fh(int)p Fe(>)164 2001 y Fh(De\256nes)h(the)f(vertical)g(spacing)h(in)f
1097 (character)h(units)f(between)h(blocks)f(of)g(sequences)i(when)164
1098 2061 y(more)e(than)g(one)g(block)h(will)f(\256t)g(on)g(a)g(page)h(-)f
1099 (default)g(is)g(0.)164 2121 y(DEFINE)p 344 2121 V 18
1100 w(COLOUR)h Fe(<)p Fh(int)p Fe(>)f(<)p Fh(\257oat)p Fe(>)g(<)p
1101 Fh(\257oat)p Fe(>)g(<)p Fh(\257oat)p Fe(>)164 2181 y
1102 Fh(DEFINE)p 344 2181 V 18 w(COLOR)164 2242 y(De\256nes)d(a)h(colour)e
1103 (-)h(the)g(\256rst)g(number)g(is)g(a)g(number)g(by)g(which)g(the)g
1104 (colour)g(will)g(be)g(referred.)164 2302 y(The)h(following)f(three)g
1105 (numbers)g(are)h(the)f(intensities)h(of)f(red,)i(green)e(and)g(blue)h
1106 (respectively)m(.)164 2362 y(Thus:)164 2422 y(DEFINE)p
1107 344 2422 V 18 w(COLOUR)j(1)g(0)f(0.2)h(0.8)949 2607 y(20)p
1108 eop
1109 %%Page: 21 22
1110 21 21 bop 164 315 a Fh(sets)19 b(colour)e(number)g(1)h(to)g(be)g(a)g
1111 (colour)g(with)f(no)h(red,)i(0.2)e(green)g(and)g(0.8)g(blue.)35
1112 b(The)164 376 y(exact)19 b(appearance)g(of)f(this)h(colour)f(will)g
1113 (depend)g(on)h(the)g(output)f(device.)37 b(If)18 b(you)g(\256nd)164
1114 436 y(suitable)d(combinations)f(of)h(colours)f(for)g(your)g(printer)n
1115 (,)h(then)g(please)g(let)g(me)g(know)f(and)h(I)164 496
1116 y(shall)e(distribute)e(your)h(suggestions)h(with)f(the)g(program.)164
1117 556 y(DO)p 239 556 15 2 v 18 w(TICKS)164 616 y(If)j(present,)i(then)f
1118 (tick)f(marks)h(are)f(drawn)h(below)f(the)h(numbers)f(at)h(the)g(top)f
1119 (of)h(the)f(page.)164 677 y(Otherwise)d(no)g(ticks)h(are)f(shown.)164
1120 737 y(NUMBER)p 379 737 V 19 w(INT)g Fe(<)p Fh(int)p Fe(>)164
1121 797 y Fh(Speci\256es)g(the)h(interval)e(for)h(writing)f(residue)h
1122 (position)g(numbers.)18 b(Default)12 b(is)h(10)164 857
1123 y(NO)p 239 857 V 18 w(NUMBERS)164 917 y(Switches)f(all)h(residue)f
1124 (numbering)f(of)o(f.)164 1050 y Ff(15.1.4)50 b(STEP)13
1125 b(2)g(COMMANDS)164 1144 y Fh(All)f(these)h(are)f(optional)g(formatting)
1126 f(commands.)164 1204 y(IMPOR)m(T)l(ANT)i(PLEASE)g(READ)g(THIS)f(NOTE:)
1127 164 1264 y(For)d(those)i(commands)f(that)f(accept)i(region)e
1128 (de\256nitions)h(\(e.g.)17 b(SURROUND)p 1547 1264 V 18
1129 w(CHARS\))10 b(it)164 1324 y(is)e(easiest)g(to)g(think)g(of)g(the)g
1130 (region)g(being)g(de\256ned)g(i)o(n)g(term)o(s)g(of)g(X)g(and)g(Y)f
1131 (coordinates,)f(where)164 1385 y(X)16 b(is)g(the)g(sequence)h(residue)f
1132 (coordinate)f(and)h(Y)g(is)g(the)g(sequence)h(number)e(coordinate.)164
1133 1445 y(Thus)h(3)f(7)f(means)i(the)f(3rd)f(residue)h(in)g(sequence)g(7.)
1134 26 b(3)15 b(7)g(12)g(42)g(means)g(the)g(rectangular)164
1135 1505 y(box)d(bounded)g(by)g(residue)h(3)f(of)g(sequence)h(7)f(and)h
1136 (residue)f(12)g(of)g(sequence)h(42.)164 1565 y(SURROUND)p
1137 441 1565 V 18 w(CHARS)f Fe(<)p Fh(string)p Fe(>)g Fh(ALL)164
1138 1625 y(Draw)g(lines)h(round,)f(but)g(not)g(between)g(the)h(characters)f
1139 (that)g(are)h(in)f(the)g(string.)18 b(e.g.)164 1685 y(SURROUND)p
1140 441 1685 V 18 w(CHARS)12 b(GP)h(ALL)164 1746 y(will)k(draw)f(lines)h
1141 (round)f(all)h(G)g(and)g(P)g(characters)g(in)g(the)g(alignment,)h(but)e
1142 (not)h(between)164 1806 y(adjacent)12 b(G)h(and)f(P)g(characters.)164
1143 1866 y(SURROUND)p 441 1866 V 18 w(CHARS)g Fe(<)p Fh(string)p
1144 Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
1145 Fe(>)g(<)p Fh(int)p Fe(>)164 1926 y Fh(Similar)j(command,)i(but)f(the)g
1146 (surrounding)f(is)h(restricted)g(to)g(the)g(region)f(de\256ned)h(by)g
1147 (the)164 1986 y(four)11 b(integers.)164 2047 y(e.g.)164
1148 2107 y(SURROUND)p 441 2107 V 18 w(CHARS)h(IL)-5 b(VW)13
1149 b(3)g(12)f(7)g(32)164 2167 y(would)17 b(surround)f(IL)-5
1150 b(VW)18 b(characters)f(that)g(occur)g(in)g(the)g(region)g(de\256ned)g
1151 (from)f(residue)164 2227 y(positions)c(3-7)g(of)g(sequences)i(12)e(to)g
1152 (32.)164 2287 y(SHADE)p 333 2287 V 18 w(CHARS)g Fe(<)p
1153 Fh(string)p Fe(>)g Fh(ALL)i Fe(<)p Fh(\257oat)p Fe(>)164
1154 2348 y Fh(Shade)e(all)g(characters)h(in)f(the)g Fe(<)p
1155 Fh(string)p Fe(>)g Fh(by)g(the)h(grey)f(value)g(given)g(by)g
1156 Fe(<)p Fh(\257oat)p Fe(>)p Fh(.)18 b(e.g.)164 2408 y(SHADE)p
1157 333 2408 V 18 w(CHARS)12 b(GP)h(ALL)g(0.5)164 2468 y(would)f(shade)h
1158 (all)f(G)h(and)f(P)g(characters)g(in)h(the)f(alignment)g(by)g(the)g
1159 (grey)g(value)h(0.5.)949 2607 y(21)p eop
1160 %%Page: 22 23
1161 22 22 bop 164 315 a Fh(SHADE)p 333 315 15 2 v 18 w(CHARS)12
1162 b Fe(<)p Fh(string)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
1163 Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(\257oat)p
1164 Fe(>)164 376 y Fh(restricts)g(the)g(shading)h(to)f(the)g(region)g
1165 (de\256ned)g(by)h(the)f(four)f(integers.)18 b(Thus)164
1166 436 y(SHADE)p 333 436 V 18 w(CHARS)12 b(IL)-5 b(VW)13
1167 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
1168 (W)g(characters)g(from)g(residues)g(3-7)g(of)g(sequences)g(12-32)g
1169 (inclusive)164 556 y(with)k(a)h(grey)f(value)g(of)g(0.7.)164
1170 616 y(FONT)p 297 616 V 18 w(CHARS)g Fe(<)p Fh(string)p
1171 Fe(>)g Fh(ALL)i Fe(<)p Fh(int)p Fe(>)164 677 y Fh(e.g.)164
1172 737 y(FONT)p 297 737 V 18 w(CHARS)e(GP)h(ALL)g(7)164
1173 797 y(would)j(use)h(font)e(7)i(to)f(write)f(out)i(all)f(G)g(and)g(P)g
1174 (characters.)31 b(Font)15 b(7)i(MUST)f(have)h(been)164
1175 857 y(de\256ned)12 b(using)g(the)h(DEFINE)p 697 857 V
1176 18 w(FONT)f(commands)h(above.)164 917 y(FONT)p 297 917
1177 V 18 w(CHARS)f Fe(<)p Fh(string)p Fe(>)g(<)p Fh(int)p
1178 Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
1179 Fe(>)g(<)p Fh(int)p Fe(>)164 978 y Fh(Similar)18 b(to)h(previous)g
1180 (command,)i(but)e(restricts)h(the)f(ef)o(fect)g(to)g(the)g(region)g
1181 (de\256ned)g(by)164 1038 y(the)d(\256rst)f(four)g(integers.)28
1182 b(The)16 b(font)f(must)h(have)g(been)g(de\256ned)f(by)h(the)g(DEFINE)p
1183 1638 1038 V 18 w(FONT)164 1098 y(command.)164 1158 y(e.g.)164
1184 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
1185 (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
1186 (and)g(W)h(characters)f(for)f(residues)i(3-9)e(of)h(sequences)h(45-)164
1187 1339 y(70)i(inclusive.)19 b(The)12 b(font)g(must)h(have)f(been)h
1188 (de\256ned)f(by)g(the)g(DEFINE)p 1416 1339 V 18 w(FONT)h(command.)164
1189 1399 y(FONT)p 297 1399 V 18 w(REGION)g Fe(<)p Fh(int)p
1190 Fe(>)e(<)p Fh(int)p Fe(>)h(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
1191 Fe(>)g(<)p Fh(int)p Fe(>)164 1459 y Fh(De\256ne)g(the)h(font)e(to)h
1192 (use)h(throughout)e(the)i(region)e(speci\256ed)i(by)f(the)h(\256rst)f
1193 (four)f(integers.)164 1519 y(e.g.)164 1579 y(FONT)p 297
1194 1579 V 18 w(REGION)i(3)f(12)g(20)g(40)h(10)164 1640 y(Use)j(font)f(10)g
1195 (for)f(residues)i(from)e(residues)i(3-20)f(of)g(sequences)h(12-40.)26
1196 b(The)16 b(font)f(must)164 1700 y(have)d(been)h(de\256ned)f(using)g
1197 (the)h(DEFINE)p 910 1700 V 18 w(FONT)f(command.)164 1760
1198 y(FONT)p 297 1760 V 18 w(RESIDUE)h Fe(<)p Fh(int)p Fe(>)f(<)p
1199 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 1820 y Fh(Set)j(the)h(font)e(for)
1200 h(use)h(with)f(a)g(single)h(residue)f(position)g(-)g(most)h(useful)f
1201 (when)h(used)f(with)164 1880 y(the)d(TEXT)i(command.)164
1202 1941 y(e.g.)164 2001 y(FONT)p 297 2001 V 18 w(RESIDUE)f(3)f(7)g(2)164
1203 2061 y(Use)i(font)g(2)f(for)g(residue)h(3)g(of)f(sequence)i(7.)23
1204 b(Font)13 b(2)h(must)g(have)g(been)g(de\256ned)f(using)h(the)164
1205 2121 y(DEFINE)p 344 2121 V 18 w(FONT)f(command.)164 2181
1206 y(LINE)g Fe(<)p Fh(string)p Fe(>)f(<)p Fh(int)p Fe(>)g(<)p
1207 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 2242 y Fh(There)i(are)h(four)e
1208 (commands)h(of)g(this)g(type)g(for)f(drawing)h(horizontal)f(or)h
1209 (vertical)g(lines)g(on)164 2302 y(the)e(alignment.)164
1210 2362 y(LINE)h(LEFT)g Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p
1211 Fe(>)g(<)p Fh(int)p Fe(>)164 2422 y Fh(Draw)g(a)h(line)f(to)g(the)g
1212 (left)g(of)g(the)g(character)g(positions)h(indicated.)164
1213 2482 y(e.g.)949 2607 y(22)p eop
1214 %%Page: 23 24
1215 23 23 bop 164 315 a Fh(LINE)13 b(LEFT)g(3)g(12)f(24)164
1216 376 y(Draw)f(a)g(vertical)g(line)g(starting)g(at)g(residue)g(3)g(of)g
1217 (sequence)h(12)f(and)g(ending)g(at)g(residue)g(3)g(of)164
1218 436 y(sequence)i(24.)164 496 y(LINE)g(T)o(OP)g(3)f(12)g(24)164
1219 556 y(Draw)i(a)h(horizontal)f(line)h(above)f(the)h(character)f
1220 (positions)h(from)f(residue)g(3)h(of)f(sequence)164 616
1221 y(12)e(to)g(residue)h(24)f(of)g(sequence)h(12.)164 677
1222 y(Similar)e(commands)h(are:)164 737 y(LINE)f(BOTT)o(OM)h
1223 Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)f(<)p Fh(int)p
1224 Fe(>)g Fh(Draw)g(a)h(line)g(at)f(bottom)g(of)h(character)f(position.)
1225 164 797 y(LINE)j(RIGHT)f Fe(<)p Fh(int)p Fe(>)g(<)p Fh(int)p
1226 Fe(>)g(<)p Fh(int)p Fe(>)g Fh(Draw)g(a)h(line)f(at)h(right)e(of)h
1227 (character)g(position.)164 857 y(BOX)p 272 857 15 2 v
1228 18 w(REGION)h Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)g(<)p
1229 Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)164 917 y Fh(Draw)h(a)h(box)f(around)
1230 g(the)g(region)g(indicated)g(by)g(the)g(four)g(integers.)164
1231 978 y(e.g.)164 1038 y(BOX)p 272 1038 V 18 w(REGION)h(2)f(5)g(30)h(7)164
1232 1098 y(W)l(ould)f(box)g(from)f(residue)i(2)f(of)g(sequence)h(5)f(to)h
1233 (residue)f(30)g(of)g(sequence)h(7.)164 1158 y(SHADE)p
1234 333 1158 V 18 w(REGION)g Fe(<)p Fh(int)p Fe(>)e(<)p Fh(int)p
1235 Fe(>)h(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(\257oat)p
1236 Fe(>)164 1218 y Fh(Shade)g(the)g(region)f(indicated)h(by)g(the)g
1237 (integers)g(with)g(the)g(grey)g(value)g(shown)g(by)g(the)g(\257oat.)164
1238 1279 y(e.g.)164 1339 y(SHADE)p 333 1339 V 18 w(REGION)h(30)f(40)g(35)g
1239 (46)h(0.2)164 1399 y(W)l(ould)f(shade)h(from)e(residue)i(30-35)e(of)h
1240 (sequences)i(40-46)d(with)h(a)h(grey)f(value)g(of)g(0.2.)164
1241 1459 y(SHADE)p 333 1459 V 18 w(RES)h Fe(<)p Fh(int)p
1242 Fe(>)f(<)p Fh(int)p Fe(>)g(<)p Fh(\257oat)p Fe(>)164
1243 1519 y Fh(Shade)g(just)h(one)f(amino)g(acid)g(with)g(the)h(grey)f
1244 (value.)164 1579 y(e.g.)164 1640 y(SHADE)p 333 1640 V
1245 18 w(RES)h(3)f(4)g(0.7)164 1700 y(Shades)h(residue)f(3)g(of)g(sequence)
1246 h(7.)19 b(\(Note:)e(this)12 b(can)h(also)g(be)f(achieved)g(with)g(the)
1247 164 1760 y(SHADE)p 333 1760 V 18 w(REGION)h(command,)f(but)g(requires)g
1248 (2)g(extra)g(numbers\))164 1820 y(TEXT)i Fe(<)p Fh(int)p
1249 Fe(>)e(<)p Fh(int)p Fe(>)g(<)p Fh(qstring)p Fe(>)164
1250 1880 y Fh(Place)g(the)h(text)f(string)g(at)g(the)g(location)g
1251 (indicated.)164 1941 y(e.g.)164 2001 y(TEXT)i(30)e(70)g("Active)h(Site)
1252 f(His")164 2061 y(would)k(put)g(the)g(text)f(Active)h(Site)g(His)h
1253 (starting)e(at)h(position)g(30)g(of)g(sequence)g(70.)30
1254 b(\(Use)164 2121 y(FONT)p 297 2121 V 18 w(RESIDUE)12
1255 b(or)g(FONT)p 721 2121 V 18 w(REGION)g(commands)g(to)g(set)g(the)g
1256 (font)f(of)h(the)f(text\).)18 b(T)m(ext)164 2181 y(added)13
1257 b(with)g(the)g(TEXT)i(command)e(will)g(not)g(be)g(split)g(across)h
1258 (page)f(breaks,)h(so)g(you)f(may)164 2242 y(in)d(some)h(circumstances)f
1259 (need)h(to)f(\256ddle)g(a)h(little)e(with)h(the)h(location/pointsize)e
1260 (for)h(the)g(text)164 2302 y(to)i(get)h(the)f(desired)g(result.)164
1261 2362 y(ID)p 220 2362 V 17 w(FONT)h(ALL)g Fe(<)p Fh(int)p
1262 Fe(>)164 2422 y Fh(Set)f(the)g(font)g(for)g(all)g(identi\256er)f(codes)
1263 i(to)f(the)h(font)e(number)h(shown)h(by)f Fe(<)p Fh(int)p
1264 Fe(>)p Fh(.)18 b(e.g.)164 2482 y(ID)p 220 2482 V 17 w(FONT)13
1265 b(ALL)g(3)949 2607 y(23)p eop
1266 %%Page: 24 25
1267 24 24 bop 164 315 a Fh(W)l(ould)12 b(set)h(all)f(the)g(identi\256er)g
1268 (codes)h(to)f(font)g(3.)164 376 y(ID)p 220 376 15 2 v
1269 17 w(FONT)h Fe(<)p Fh(int)p Fe(>)f(<)p Fh(int)p Fe(>)164
1270 436 y Fh(Set)g(the)g(font)g(for)g(a)g(speci\256c)h(identi\256er)e(to)h
1271 (font)g(number)m(.)18 b(e.g.)164 496 y(ID)p 220 496 V
1272 17 w(FONT)13 b(12)f(4)164 556 y(Use)h(font)f(4)g(for)f(the)i(identifer)
1273 e(of)h(sequence)h(12,)g(default)e(font)h(for)g(all)g(other)g
1274 (identi\256ers.)164 616 y(SUB)p 264 616 V 18 w(CHARS)g(ALL)i
1275 Fe(<)p Fh(char)p Fe(>)e(<)p Fh(char)p Fe(>)164 677 y
1276 Fh(Substitute)g(the)g(characters)g(indicated.)164 737
1277 y(e.g.)164 797 y(SUB)p 264 797 V 18 w(CHARS)g(ALL)i(+)e(*)164
1278 857 y(would)g(change)g(all)h(occurences)f(of)g(+)h(to)f(*)h(in)f(the)g
1279 (alignment.)164 917 y(SUB)p 264 917 V 18 w(CHARS)g Fe(<)p
1280 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p
1281 Fh(int)p Fe(>)g(<)p Fh(char)p Fe(>)g(<)p Fh(char)p Fe(>)164
1282 978 y Fh(restrict)g(the)g(substitution)g(to)g(the)h(region)e(shown.)164
1283 1038 y(e.g.)164 1098 y(SUB)p 264 1098 V 18 w(CHARS)h(1)h(1)f(7)g(8)h
1284 (\045)g(*)164 1158 y(would)e(substitute)h(*)g(for)f(\045)h(from)f
1285 (residue)h(1-7)f(of)g(sequences)i(1-8.)18 b(NOTE:)12
1286 b(T)m(o)g(substitute)164 1218 y(for)17 b(or)h(with)g(the)g(space)h
1287 (character)e(use)i(the)f(word)g(SP)-5 b(ACE.)19 b(e.g.)36
1288 b(to)18 b(change)g(all)g(space)164 1279 y(characters)12
1289 b(to)h(-.)164 1339 y(SUB)p 264 1339 V 18 w(CHARS)f(ALL)i(SP)-5
1290 b(ACE)12 b(-)164 1399 y(SUB)p 264 1399 V 18 w(ID)g Fe(<)p
1291 Fh(int)p Fe(>)g(<)p Fh(qstring)p Fe(>)164 1459 y Fh(Replace)h(the)f
1292 (numbered)g(identi\256er)f(by)h(the)h(string.)18 b(e.g.)164
1293 1519 y(SUB)p 264 1519 V 18 w(ID)12 b(34)g("Predicted)g(Secondary)g
1294 (Structure")164 1579 y(would)e(replace)h(whatever)f(the)h(identi\256er)
1295 e(of)i(sequence)g(34)g(was,)h(by)e(the)h(text)f(shown.)18
1296 b(This)164 1640 y(is)f(useful)f(when)g(used)h(in)f(conjunction)g(with)g
1297 (the)h(ADD)p 1185 1640 V 17 w(SEQ)g(command)f(shown)g(under)164
1298 1700 y(the)c(STEP)h(1)f(commands.)164 1760 y(INVERSE)p
1299 377 1760 V 18 w(CHARS)i Fe(<)p Fh(string)p Fe(>)f Fh(ALL/Range)i
1300 (\(similar)d(syntax)i(to)f(FONT)p 1524 1760 V 18 w(CHARS)h(but)164
1301 1820 y(no)e(font)g(number\))164 1880 y(Print)g(the)i(selected)f
1302 (characters)h(in)f(white.)21 b(This)14 b(clearly)f(will)g(only)g(work)g
1303 (if)f(you)i(\256rst)e(use)164 1941 y(the)f(SHADE)p 405
1304 1941 V 18 w(CHARS)g(command)g(to)g(shade)h(the)f(characters)g(with)g
1305 (something)g(other)f(than)164 2001 y(white.)164 2061
1306 y(CCOL)p 299 2061 V 19 w(CHARS)i Fe(<)p Fh(string)p Fe(>)g
1307 Fh(ALL)h Fe(<)p Fh(int)p Fe(>)164 2121 y Fh(Colour)f(all)g(characters)g
1308 (in)h(the)f Fe(<)p Fh(string)p Fe(>)g Fh(by)g(the)g(colour)g(de\256ned)
1309 g(by)g Fe(<)p Fh(int)p Fe(>)p Fh(.)164 2181 y(e.g.)164
1310 2242 y(CCOL)p 299 2242 V 19 w(CHARS)g(GP)g(ALL)i(12)164
1311 2302 y(would)c(colour)g(all)g(G)h(and)f(P)g(characters)h(in)f(the)h
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1314 1002 2362 V 19 w(COLOUR)h(command.)164 2422 y(CCOL)p
1315 299 2422 V 19 w(CHARS)f Fe(<)p Fh(string)p Fe(>)g(<)p
1316 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p
1317 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 2482 y Fh(restricts)g(the)g
1318 (colouring)g(to)g(the)g(region)g(de\256ned)g(by)g(the)h(four)e
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1320 %%Page: 25 26
1321 25 25 bop 164 315 a Fh(CCOL)p 299 315 15 2 v 19 w(CHARS)12
1322 b(IL)-5 b(VW)13 b(3)g(12)f(7)g(32)g(7)164 376 y(would)21
1323 b(colour)f(I)h(L)h(V)f(and)h(W)f(characters)g(from)f(residues)i(3-7)f
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1325 (7.)164 496 y(SCOL)p 294 496 V 18 w(CHARS:)e(This)h(has)g(identical)f
1326 (syntax)g(to)g(SCOL)p 1170 496 V 18 w(CHARS,)h(but)f(colours)g(the)g
1327 (back-)164 556 y(ground)j(of)f(the)i(character)n(,)f(rather)g(than)g
1328 (the)g(letter)g(itself.)164 616 y(COLOUR)p 371 616 V
1329 19 w(REGION)g Fe(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p
1330 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164
1331 677 y Fh(COLOR)p 335 677 V 19 w(REGION)164 737 y(Colour)j(the)g(region)
1332 g(indicated)f(by)i(the)f(integers)g(with)g(the)g(colour)g(number)f
1333 (given)h(as)h(the)164 797 y(last)d(number)m(.)164 857
1334 y(e.g.)164 917 y(COLOUR)p 371 917 V 19 w(REGION)f(30)h(40)f(35)g(46)g
1335 (2)164 978 y(W)l(ould)g(colour)g(from)f(residue)h(30-35)g(of)g
1336 (sequences)h(40-46)f(with)g(the)g(colour)g(2.)164 1038
1337 y(COLOUR)p 371 1038 V 19 w(RES)g Fe(<)p Fh(int)p Fe(>)g(<)p
1338 Fh(int)p Fe(>)g(<)p Fh(int)p Fe(>)164 1098 y Fh(Colour)g(just)g(one)h
1339 (amino)f(acid)g(with)g(the)g(de\256ned)g(colour)m(.)164
1340 1158 y(e.g.)164 1218 y(COLOUR)p 371 1218 V 19 w(RES)g(3)h(4)f(7)164
1341 1279 y(Colours)21 b(residue)f(3)h(of)g(sequence)g(7.)44
1342 b(\(Note:)34 b(this)21 b(can)g(also)h(be)f(achieved)g(with)f(the)164
1343 1339 y(COLOUR)p 371 1339 V 19 w(REGION)12 b(command,)h(but)f(requires)g
1344 (2)g(extra)g(numbers\))164 1486 y Fb(15.2)59 b(AMPS)16
1345 b(Block)e(\256le)g(format)164 1580 y Fh(The)f(\256rst)e(part)h(of)g(a)g
1346 (block-\256le)g(contains)g(the)g(identi\256er)f(codes)i(of)f(the)g
1347 (sequences)h(that)f(are)164 1640 y(to)g(follow)m(.)17
1348 b(Each)c(code)g(is)g(pre\256xed)e(by)i(the)f Fe(>)g Fh(symbol,)h(codes)
1349 g(must)f(not)g(contain)g(spaces.)164 1700 y(e.g.)164
1350 1802 y Fd(>HAHU)164 1862 y(>Trypsin)164 1922 y(>A0046)164
1351 1982 y(>Seq1)164 2144 y Fh(etc.)164 2204 y(ALSCRIPT)k(counts)f(the)h
1352 (number)e(of)h Fe(>)h Fh(symbols)f(in)g(the)h(beginning)e(of)h(the)h
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1354 b(The)15 b(*)f(signals)h(the)f(beginning)f(of)h(the)g(multiple)g
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1356 b(Y)f(,)16 b(thus)e(columns)h(are)f(individual)f(sequences,)k(whilst)d
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1358 b(*)g(symbol)g(must)g(lie)g(over)f(the)h(\256rst)g(sequence.)19
1359 b(A)12 b(further)e(star)i(in)164 2445 y(the)j(same)g(column)f(signals)h
1360 (the)g(end)f(of)g(the)h(alignment.)25 b(ALSCRIPT)15 b(uses)g(the)g
1361 (number)949 2607 y(25)p eop
1362 %%Page: 26 27
1363 26 26 bop 164 315 a Fh(of)13 b Fe(>)g Fh(symbols)h(at)g(the)f
1364 (beginning)g(of)g(the)g(\256le)h(to)f(work)g(out)g(how)g(many)h
1365 (columns)f(to)g(read)164 376 y(from)h(the)h(*)f(position.)26
1366 b(It)14 b(is)h(therefore)f(important)g(that)g(the)h(only)g
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1368 (de\256ne)f(the)h(identi\256ers,)g(and)g(the)g(only)f(*)h(symbols)g
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1370 g(multiple)g(alignment.)17 b(The)12 b(block)f(\256le)g(can)h(contain)f
1371 (additional)g(text,)164 556 y(providing)16 b(that)i(there)f(are)h(no)f
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1373 (used)g(to)164 616 y(de\256ne)12 b(the)g(identi\256ers)g(or)g
1374 (alignment)g(start)g(and)g(end.)164 677 y(A)g(simple,)h(small)g
1375 (block-\256le)e(is)i(shown)f(here.)164 791 y Fd(>Seq_1)164
1376 851 y(>A0231)164 911 y(>HAHU)164 971 y(>Four_Alpha)164
1377 1032 y(>Globin)164 1092 y(>GLobin_C)164 1152 y(*)164
1378 1212 y(ARNDLQ)164 1272 y(AAAAAA)164 1333 y(PPPPPP)164
1379 1393 y(PP)30 b(PPP)164 1453 y(WW)g(WWW)164 1513 y(LLLLLL)164
1380 1573 y(IIVVLL)164 1633 y(*)164 1781 y Fb(15.3)59 b(PostScript)14
1381 b(Fonts)164 1874 y Fd(Times-Roman,)164 1935 y(Times-Italic,)164
1382 1995 y(Times-Bold,)164 2055 y(Times-BoldItalic,)164 2115
1383 y(Helvetica,)164 2175 y(Helvetica-Oblique,)164 2236 y(Helvetica-Bold,)
1384 164 2296 y(Helvetica-BoldOblique,)164 2356 y(Courier,)164
1385 2416 y(Courier-Oblique,)164 2476 y(Courier-Bold)949 2607
1386 y Fh(26)p eop
1387 %%Page: 27 28
1388 27 27 bop 164 315 a Fd(Courier-BoldOblique,)164 376 y(AvantGarde-Book,)
1389 164 436 y(AvantGarde-BookOblique,)164 496 y(AvantGarde-Demi,)164
1390 556 y(AvantGarde-DemiOblique,)164 616 y(Bookman-Demi,)164
1391 677 y(Bookman-DemiItalic,)164 737 y(Bookman-Light,)164
1392 797 y(Bookman-LightItalic,)164 857 y(Helvetica-Narrow,)164
1393 917 y(Helvetica-Narrow-Bold,)164 978 y(Helvetica-Narrow-BoldOblique,)
1394 164 1038 y(Helvetica-Narrow-Oblique,)164 1098 y
1395 (NewCenturySchblk-Roman,)164 1158 y(NewCenturySchlbk-Bold,)164
1396 1218 y(NewCenturySchblk-Italic,)164 1279 y
1397 (NewCenturySchblk-BoldItalic,)164 1339 y(Palatino-Roman,)164
1398 1399 y(Palatino-Bold,)164 1459 y(Palatino-Italic,)164
1399 1519 y(Palatino-BoldItalic)164 1579 y(ZapfChancery-MediumItalic.)164
1400 1640 y(Symbol)164 1787 y Fb(15.4)59 b(386)15 b(DOS)g(installation)164
1401 1881 y Fh(IMPOR)m(T)l(ANT)d(-)e(The)i(programs)e(on)h(this)g(disk)h
1402 (will)e(ONL)-5 b(Y)12 b(WORK)f(on)g(a)g(PC)g(with)g(a)g(386)164
1403 1941 y(or)h(better)g(processor)m(.)18 b(See)13 b(the)f(T)m(echnical)g
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1406 g(hard)g(disk.)19 b(e.g.)g(mkdir)11 b(ALSCRIPT)l(.)224
1407 2217 y(2.)25 b(Copy)12 b(the)h(Contents)f(of)g(the)g(\257oppy)g(disk)h
1408 (into)f(this)g(directory)m(.)405 2339 y Fd(e.g.)90 b(copy)29
1409 b(a:*.*)g(c:\\alscript.)224 2462 y Fh(3.)c(Edit)12 b(your)g(AUT)o
1410 (OEXEC.BA)-6 b(T)16 b(\256le)c(and)g(add)949 2607 y(27)p
1411 eop
1412 %%Page: 28 29
1413 28 28 bop 316 315 a Fd(C:\\ALSCRIPT)28 b(to)i(your)g(path.)224
1414 438 y Fh(4.)25 b(Edit)d(your)g(AUT)o(OEXEC.BA)-6 b(T)26
1415 b(\256le)c(and)g(add)g(the)h(following)e(two)h(lines.)49
1416 b(set)286 498 y(DOS4GVM=@ALSCRIPT)l(.VMC)14 b(set)e(DOS4G=quiet)164
1417 612 y(The)h(\256rst)f(line)g(is)g(an)g(instruction)g(to)g(read)g
1418 (instructions)g(from)f(the)h(\256le)g(ALSCRIPT)l(.VMC.)164
1419 672 y(This)k(sets)g(up)g(a)g(permanent)e(swap)i(\256le)g(on)f(your)g
1420 (hard)g(disk.)28 b(By)16 b(default,)g(the)f(swap)h(\256le)164
1421 733 y(is)d(about)g(12MBytes)h(in)f(size.)20 b(If)13 b(you)f(do)h(not)g
1422 (have)g(this)g(much)g(free)f(space)i(on)f(your)f(disk,)164
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1424 h(swap)g(\256le)f(size,)j(or)d(alternatively)m(,)164
1425 853 y(do)d(not)g(put)g(this)h(line)f(in)g(your)g(autoexec.bat.)164
1426 913 y(The)g(programs)f(will)g(run)f(without)h(this)h(swap)g(\256le,)f
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1429 (you)e(have)i(installed.)17 b(I)11 b(have)g(only)164
1430 1034 y(tested)i(this)f(program)g(on)g(a)h(486/33)f(with)g(8MBytes)h
1431 (RAM)g(and)f(a)h(386/33)f(with)g(4MBytes)164 1094 y(so)18
1432 b(I)g(do)f(not)h(know)f(the)h(practical)g(limitations)f(of)g(machines)h
1433 (with)f(smaller)h(memories.)164 1154 y(Any)12 b(feedback)g(would)g(be)h
1434 (appreciated.)164 1214 y(5.)46 b(T)m(ype)22 b(AUT)o(OEXEC.BA)-6
1435 b(T)24 b(to)e(initialise)f(the)h(changes,)j(or)c(better)g(still,)j
1436 (reset)e(the)164 1274 y(computer)m(.)164 1335 y(6.)17
1437 b(Y)-5 b(ou)10 b(should)g(now)g(be)g(able)g(to)f(run)h(all)f(three)h
1438 (programs)f(in)h(the)f(package)i(from)d(anywhere)164
1439 1395 y(on)13 b(your)f(disk.)19 b(msf2blc,)13 b(clus2blc)f(and)h
1440 (alscript.)19 b(If)12 b(you)g(get)h(memory)f(allocation)g(errors)164
1441 1455 y(when)20 b(you)g(try)g(to)g(run)f(alscript,)k(then)d(use)g(the)g
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1444 b(to)f(reduce)g(the)h(default)f(limits.)22 b(If)13 b(the)g(program)g
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1451 (and)f(you)g(are)h(not)f(using)g(the)g(virtual)g(memory)164
1452 1816 y(option)j(discussed)h(above,)h(then)f(try)f(adding)g(the)g(line)g
1453 (set)h(DOS4GVM=@\256lename)f(to)164 1876 y(your)12 b(autoexec.bat)h
1454 (\256le.)20 b(If)12 b(you)g(don')o(t)g(have)h(enough)g(disk)g(space)g
1455 (to)g(do)f(this,)i(then)e(buy)h(a)164 1936 y(bigger)f(disk,)h(or)f
1456 (more)f(memory)m(.)164 2084 y Fb(15.5)59 b(TECHNICAL)15
1457 b(NOTES)164 2177 y Fh(The)i(executables)g(included)f(in)h(this)f
1458 (package)h(were)f(compiled)h(with)f(the)g(W)-6 b(A)g(TCOM)19
1459 b(C)164 2238 y(compiler)m(.)h(This)13 b(is)h(a)f(full)f(32)h(bit)g
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1468 (extra)g(program)f(called)h(a)h(dos)f(extender)g(is)949
1469 2607 y(28)p eop
1470 %%Page: 29 30
1471 29 29 bop 164 315 a Fh(required)9 b(-)h(this)h(is)g(called)f(DOS4GW)-5
1472 b(.EXE.)12 b(DOS4GW)e(is)h(automatically)e(invoked)h(every)164
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1476 583 y Fb(15.6)59 b(Unix)15 b(Installation)164 677 y Fh(ALSCRIPT)c(is)h
1477 (distributed)e(with)h(executables)g(for)g(Sun)f(\(SunOS)g(4.1.3\),)i
1478 (Silicon)f(Graph-)164 737 y(ics)k(\(IRIX)f(5.3\),)i(DEC)g(ALPHA)f
1479 (OSF/1)f(and)h(Sun)f(Solaris)h(\(2.4\).)25 b(The)16 b(executables)f
1480 (are)164 797 y(stored)f(in)g(the)h(subdirectories)f(bin/sun,)h
1481 (bin/sgi,)g(bin/osf)f(and)g(bin/sol.)24 b(If)14 b(these)h(are)f(OK)164
1482 857 y(for)f(your)g(system,)h(then)g(just)f(add)h(the)f(apporpriate)g
1483 (directory)f(to)i(your)f(path,)h(or)f(put)g(links)164
1484 918 y(to)f(/usr/local/bin)g(or)f(somewhere)i(that)f(is)h(on)f(all)g
1485 (users)h(paths.)164 978 y(The)k(source)g(code)g(for)f(ALSCRIPT)i(is)f
1486 (contained)f(in)h(a)g(directory)f(hierarchy)m(.)31 b(The)17
1487 b(top)164 1038 y(directory)h(contains)g(a)h(README)i(\256le)d(and)h
1488 (the)f(BUILD)h(script.)38 b(Subdirectories)17 b(are:)164
1489 1098 y Ff(examples)12 b Fh(which)g(contains)g(example)f(command)g(and)h
1490 (alignment)f(\256les,)h Ff(doc)g Fh(which)f(con-)164
1491 1158 y(tains)16 b(L)286 1151 y Fa(A)307 1158 y Fh(T)329
1492 1174 y(E)354 1158 y(Xand)g(PostScript)e(copies)i(of)f(the)h(manual)f(-)
1493 g(a)h(subdirectory)f(of)g(this)h(contains)164 1218 y(an)j(HTML)g
1494 (version)g(of)f(the)g(manual,)i(and)f Ff(sr)o(c)g Fh(which)g(contains)f
1495 (the)h(source)f(code)h(and)164 1279 y(Make\256les)d(for)e(the)h
1496 (package.)27 b(There)15 b(may)g(also)g(be)h(a)f(directory)f(called)h
1497 Ff(bin)p Fh(.)26 b(If)14 b(present)164 1339 y(this)f(will)f(contain)g
1498 (subdirectories)g(with)h(executables)g(for)f(the)g(programs)g(in)h(the)
1499 f(package.)164 1399 y(Make\256les)j(to)f(build)g(alscript,)g(msf2blc,)h
1500 (clus2blc)f(and)h(alsnum)f(are)g(included)g(in)g(the)g
1501 Ff(sr)o(c)164 1459 y Fh(directory)m(.)37 b(V)-6 b(ersions)20
1502 b(for)f(Sun)f(\(acc)i(compiler)e(.sun\),)k(Silicon)c(Graphics)h
1503 (\(.sgi\),)i(DEC)164 1519 y(OSF/1)12 b(\(.osf\))f(are)i(included.)164
1504 1580 y(There)i(is)g(a)g(utility)e(csh)i(script)g(called)f(BUILD.)i
1505 (Simply)d(type)i(./BUILD)g(sun)g(to)f(compile)164 1640
1506 y(alscript)e(on)h(the)g(Sun,)g(./BUILD)g(sgi)g(for)f(Silicon)g
1507 (Graphics)h(or)f(BUILD)h(gcc)g(for)f(use)h(with)164 1700
1508 y(gcc)i(compiler)m(.)26 b(See)16 b(instructions)e(in)h(the)g(\256le)g
1509 (BUILD.)h(The)g(BUILD)f(script)g(will)g(create)164 1760
1510 y(a)e(/bin)f(directory)g(and)h(subdirecotry)f(if)g(not)h(already)g
1511 (present.)19 b(Y)-5 b(ou)13 b(can)g(create)g(make\256les)164
1512 1820 y(for)f(dif)o(ferent)f(computers)h(and)g(the)g(BUILD)h(script)f
1513 (should)g(still)h(function.)164 1968 y Fb(15.7)59 b(V)-8
1514 b(AX/VMS)16 b(Installation)164 2061 y Fh(The)c(standard)f(V)-6
1515 b(AX)10 b(C)i(compiler)e(is)h(not)g(ANSI.)g(Accordingly)m(,)g(ALSCRIPT)
1516 g(will)g(require)164 2122 y(changes)i(to)f(the)g(source)h(code)f(to)h
1517 (compile)f(on)g(a)g(V)-6 b(AX.)164 2182 y(The)12 b(DEC)g(C++)g
1518 (compiler)f(works)g(OK)g(for)g(alscript.)18 b(Alscript)11
1519 b(will)g(also)g(compile)g(on)h(Dec)164 2242 y(ALPHA)g(under)g(OpenVMS.)
1520 h(A)f(descrip.mms)h(\256le)f(is)h(included)f(for)f(this)i(purpose.)164
1521 2302 y Fc(W)m(ARNING:)g(I've)f(not)g(tested)h(V)-6 b(ersion)13
1522 b(2.0)g(of)f(ALSCRIPT)h(on)f(VMS)949 2607 y Fh(29)p eop
1523 %%Page: 30 31
1524 30 30 bop 164 315 a Fb(15.8)59 b(Alternative)13 b(ways)i(of)g(invoking)
1525 g(ALSCRIPT)164 409 y Fh(The)f(documentation)e(above)h(describes)h(the)f
1526 (interactive)f(mode)h(of)g(running)f(ALSCRIPT)l(.)164
1527 469 y(However)n(,)i(it)f(may)h(be)g(more)f(convenient)g(to)g(run)g(the)
1528 h(program)e(as)j(a)e(pipe)h(under)f(Unix)g(or)164 530
1529 y(MS-DOS.)f(Examples)h(are)f(shown)h(here.)164 590 y(ALSCRIPT)g(is)f(a)
1530 h(program)e(for)g(producing)g(pretty)h(versions)g(of)g(multiple)g
1531 (sequence)h(alig-)164 650 y(ments.)29 b(ALSCRIPT)16 b(will)f(also)h
1532 (format)f(single)h(sequences.)30 b(A)15 b(full)g(description)h(of)f
1533 (the)164 710 y(program)c(is)i(given)f(in)g(the)h(\256le)f
1534 ("alscript.doc".)164 770 y(W)l(ays)h(of)f(running)f(alscript:)224
1535 884 y(1.)25 b(Interactive)13 b(mode:)21 b(just)13 b(type)h(alscript.)23
1536 b(Y)-5 b(ou)14 b(will)f(be)h(prompted)f(for)g(a)h(command)286
1537 945 y(\256le)h(name.)27 b(The)16 b(command)f(\256le)g(will)g(de\256ne)g
1538 (the)g(AMPS)g(bloc\256le,)h(and)f(name)g(of)286 1005
1539 y(the)d(\256le)g(to)h(store)f(the)g(PostScript)f(output)h(-)g(see)h
1540 (alscript.doc)g(for)e(details.)224 1107 y(2.)25 b(alscript)12
1541 b Fe(<)p Fh(command)p 683 1107 15 2 v 17 w(\256le)p Fe(>)g
1542 Fh(has)g(same)h(ef)o(fect)f(as)g(1,)h(But)f(does)h(not)f(prompt)f(for)g
1543 (the)286 1167 y(command)h(\256le)g(e.g.)19 b(alscript)12
1544 b(example1.als)224 1268 y(3.)25 b(alscript)13 b(-q)h
1545 Fe(<)f(<)p Fh(bloc\256le)p Fe(>)g(>)h(<)p Fh(PostScript)p
1546 Fe(>)f Fh(Quick)g(mode)h(-)f(uses)h(default)g(com-)286
1547 1329 y(mands,)g(reads)g(alignment)f(from)g(stdin,)h(writes)f
1548 (PostScript)g(to)g(stdout.)22 b(This)14 b(mode)286 1389
1549 y(creates)f(a)f(command)g(\256le)g(called)h(ALPSQ.COM.)286
1550 1470 y(e.g.)19 b(alscript)12 b(-q)g Fe(<)g Fh(example1.blc)h
1551 Fe(>)f Fh(example1.ps)224 1571 y(4.)25 b(alscript)12
1552 b(-f)g Fe(<)p Fh(command)p 729 1571 V 17 w(\256le)p Fe(>)g
1553 Fh(Similar)f(ef)o(fect)h(to)g(2.)224 1673 y(5.)25 b(alscript)16
1554 b(-f)g Fe(<)p Fh(command)p 737 1673 V 17 w(\256le)p Fe(>)g
1555 Fh(-s)h(Silent)e(operation:)25 b(No)17 b(messages)g(are)g(written)286
1556 1733 y(to)e(stderr)n(,)g(unless)g(fatal.)26 b(Silent)14
1557 b(operation)g(may)h(be)g(toggled)f(by)h(the)f(silent)p
1558 1657 1733 V 18 w(mode)286 1794 y(command)e(in)g(the)g(command)g
1559 (\256le.)224 1895 y(6.)25 b(alscript)8 b(-f)g Fe(<)p
1560 Fh(command)p 721 1895 V 18 w(\256le)p Fe(>)g Fh(-p)h
1561 Fe(<)f(<)p Fh(bloc\256le)p Fe(>)h(>)f(<)p Fh(PostScript)p
1562 Fe(>)g Fh(Make)h(alscript)286 1955 y(work)j(like)h(a)g(pipe)f(-)h
1563 (bloc\256le)f(is)h(read)g(from)e(stdin,)i(postscript)g(is)g(written)f
1564 (to)h(stdout.)286 2016 y(Messages)h(are)e(written)g(to)g(stderr)m(.)18
1565 b(T)m(o)13 b(supress)g(messages)g(include)f(the)h(-s)f(\257ag)g(too)286
1566 2097 y(e.g.)19 b(alscript)12 b(-f)g(example1.als)g(-p)g(-s)h
1567 Fe(<)f Fh(example1.blc)h Fe(>)f Fh(example1.ps)164 2211
1568 y(Using)f(alscript)g(as)h(a)f(pipe)g(has)h(the)f(advantage)g(of)g
1569 (allowing)g(the)g(bloc\256le)g(to)g(be)g(created)g(on)164
1570 2271 y(the)h(\257y)g(by)g(the)h(programs)e(msf2blc)h(or)g(clus2blc.)18
1571 b(For)12 b(example)g(if)g(we)g(have)h(a)f(GCG)h(.msf)164
1572 2331 y(\256le)d(called)g("pileup.msf")h(we)f(can)h(run)f(alscript)g
1573 (with)g(default)f(shading/fonts)h(and)g(send)h(the)164
1574 2391 y(results)h(straight)g(to)h(the)f(PostScript)f(printer)g("lpr")i
1575 (as)g(follows:)164 2451 y(msf2blc)f(-q)g Fe(<)p Fh(pileup.msf)g(|)g
1576 (alscript)g(-q)g(-s)h(|)f(lpr)949 2607 y(30)p eop
1577 %%Page: 31 32
1578 31 31 bop 164 315 a Fb(15.9)59 b(Pr)o(ogram)13 b(Crashes)i(and)g(Known)
1579 g(Bugs)164 409 y Fh(W)l(e've)10 b(used)h(ALSCRIPT)g(on)g(Sun)f(W)l
1580 (orkstations)g(and)h(Silicon)f(Graphics)g(for)g(some)h(time,)164
1581 469 y(with)i(very)f(lar)o(ge)h(alignments)g(and)g(command)g(\256les)g
1582 (with)g(thousands)g(of)g(commands.)20 b(All)164 530 y(seems)13
1583 b(to)f(work)g(OK,)h(the)f(program)g(has)g(not)h(crashed)f(on)g(us)h(at)
1584 g(all!!)164 590 y(However)n(,)f(the)g(command)f(interpreter)f(in)i
1585 (ALSCRIPT)g(is)g(very)g(simple)g(and)f(the)h(program)164
1586 650 y(will)f(crash)g(if)g(you)g(give)g(any)g(command)g(the)g(wrong)g
1587 (number)f(of)h(ar)o(guments)g(\(e.g.)18 b(leaving)164
1588 710 y(out)12 b(the)g(shade)h(value)g(in)f(a)g(shade)p
1589 761 710 15 2 v 19 w(chars)g(command\).)164 770 y(If)h(you)g(do)h(make)g
1590 (the)f(program)g(crash,)h(have)g(checked)g(all)f(the)h(documentation)f
1591 (and)h(your)164 830 y(numbers,)d(and)f(the)g(program)f(still)h
1592 (crashes.)19 b(Then)10 b(send)h(me)f(the)g(command)g(\256le)g(and)g
1593 (block)164 891 y(\256le)i(that)g(causes)i(the)e(crash)h(and)f(I)g(will)
1594 g(try)g(to)g(investigate.)164 951 y(Suggestions)g(for)g(improvements)f
1595 (to)h(the)h(program)e(are)h(always)h(welcome.)164 1098
1596 y Fb(15.10)59 b(W)o(ish)15 b(List)g(for)f(next)g(version!!)164
1597 1192 y Fh(A)d(command)f(interpreter)f(that)i(does)g(more)f(error)g
1598 (checking)g(will)g(be)h(included.)18 b(Currently)m(,)164
1599 1252 y(no)13 b(checking)g(is)g(done)g(to)g(make)g(sure)g(that)g(the)g
1600 (correct)g(number)f(of)g(ar)o(guments)h(are)g(given)164
1601 1312 y(to)f(a)h(command.)164 1372 y(Sequences)j(will)f(be)h(able)g(to)f
1602 (be)h(given)g(unique)f(labels)h(and)g(region)f(commands)g(refer)g(to)
1603 164 1433 y(these)c(labels)g(or)f(ranges)h(of)f(labels.)18
1604 b(This)12 b(will)e(permit)g(a)h(sequence)g(to)f(be)h(deleted)g(or)f
1605 (added)164 1493 y(to)i(the)h(alignment)e(without)h(having)g(to)g
1606 (update)g(the)h(.als)g(\256le.)164 1553 y(The)18 b(relative)f
1607 (numbering)f(option)g(will)h(be)h(extended)f(to)g(allow)g(numbering)f
1608 (relative)h(to)164 1613 y(a)f(position.)29 b(e.g.)h(456+7)16
1609 b(would)g(be)g(7)g(residues)g(after)g(position)g(456.)29
1610 b(This)17 b(will)e(allow)164 1673 y(annotation)9 b(of)g(positions)h
1611 (that)g(may)f(be)h(in)g(insertions)f(relative)h(to)f(the)h(reference)f
1612 (sequence.)164 1733 y(Special)h(TEXT)h(commands)f(will)g(be)g(extended)
1613 g(to)g(allow)g(alternative)f(shapes)i(to)f(be)g(drawn)164
1614 1794 y(and)i(scaled)h(in)f(various)h(ways.)164 1854 y(T)n(ree)21
1615 b(drawing)e(and)h(generalised)h(graphics.)41 b(An)20
1616 b(option)g(to)g(draw)g(arbitrary)f(lines)h(on)164 1914
1617 y(an)f(alignment)f(will)h(be)g(added.)39 b(This)19 b(will)g(permit)f
1618 (line)h(graphics)g(to)g(be)g(added)g(to)g(an)164 1974
1619 y(alignment.)d(The)8 b(initial)g(reason)g(for)g(this)g(will)g(be)g(to)g
1620 (show)g(dendrograms)g(\(trees\))g(alongside)164 2034
1621 y(the)k(alignment,)g(but)h(simple)f(line)g(graphs)g(could)g(also)h(be)g
1622 (plotted)e(under)h(the)h(alignment.)164 2095 y(Fiddle)c(factors)h(will)
1623 g(be)g(introduced)f(to)h(allow)g(\256ne)g(positioning)g(of)f
1624 (individual)h(characters.)164 2155 y(For)h(example,)h(if)e(you)i(like)f
1625 (your)g(\252I\272)g(characters)g(to)h(be)f(centred)g(rather)g(than)g
1626 (left)g(justi\256ed,)164 2215 y(this)h(will)g(be)h(possible.)164
1627 2275 y(In)h(single)p 342 2275 V 18 w(page)h(mode,)h(it)e(will)g(be)h
1628 (possible)g(to)g(add)g(arbitrary)e(text)h(to)h(an)g(alignment)f(for)164
1629 2335 y(\256nal)e(annotation,)g(e.g.)19 b(titles)12 b(etc.)164
1630 2396 y(V)-6 b(ariable)12 b(height/width)g(sequence)h(lines)f(will)g(be)
1631 h(permitted)e(\(maybe\).)949 2607 y(31)p eop
1632 %%Page: 32 33
1633 32 32 bop 164 315 a Fb(15.1)m(1)59 b(Acknowledgements)164
1634 409 y Fh(I)19 b(thank)g(all)h(those)g(who)f(have)h(emailed)f(me)h(with)
1635 f(suggestions)h(for)e(improvements)h(to)164 469 y(alscript.)e(I've)10
1636 b(tried)g(to)g(include)h(some)f(of)g(these)h(in)g(the)f(current)g
1637 (distribution)f(\(e.g.)18 b(screen-)164 530 y(ing\).)164
1638 677 y Fb(15.12)59 b(Refer)o(ences)164 831 y Fd(1.)h(Barton,)29
1639 b(G.)g(J.)h(\(1993\),)164 891 y("ALSCRIPT)f(A)h(tool)f(to)h(format)f
1640 (multiple)g(sequence)g(alignments",)164 951 y(Protein)g(Engineering,)59
1641 b(Volume)29 b(6,)g(No.)h(1,)g(pp.37-40.)164 1071 y(2.)60
1642 b(Barton,)29 b(G.)g(J.)h(\(1990\),)313 1132 y("Protein)f(Multiple)g
1643 (Sequence)g(Alignment)g(and)h(Flexible)f(Pat-)164 1192
1644 y(tern)g(Matching",)164 1252 y(Methods)g(in)h(Enzymology,)313
1645 1312 y(183,403-428.)164 1433 y(3.)60 b(Barton,)29 b(G.)g(J.)h(and)g
1646 (Sternberg,)e(M.)i(J.)g(E.)f(\(1987\),)313 1493 y("A)h(Strategy)f(for)h
1647 (the)f(Rapid)g(Multiple)g(Alignment)g(of)h(Pro-)164 1553
1648 y(tein)f(Sequences:)433 1613 y(Confidence)g(Levels)g(From)g(Tertiary)g
1649 (Structure)g(Comparisons",)164 1673 y(Journal)g(of)h(Molecular)f
1650 (Biology,)313 1733 y(198,327-337)164 1854 y(4.)h(Higgins,)f(D.)g(G.)h
1651 (and)g(Sharp,)f(P.)g(M.)h(\(1989\),)313 1914 y("Fast)g(and)f(sensitive)
1652 g(multiple)g(sequence)g(alignments)g(on)h(a)f(microcomputer",)164
1653 1974 y(CABIOS,)313 2034 y(5,151--153)164 2155 y(5.)h(Devereux,)f(J.)g
1654 (Haeberli,)g(P.)h(Smithies,)f(O.)g(\(1984\),)313 2215
1655 y("A)h(comprehensive)f(set)g(of)h(sequence)f(analysis)g(programs)g(for)
1656 g(the)h(VAX",)164 2275 y(Nucleic)f(Acids)g(Res.)313 2335
1657 y(12,)h(387-395)164 2456 y(6.)g(Livingstone,)e(C.)i(D.)g(and)f(Barton,)
1658 g(G.)h(J.)f(\(1993\),)949 2607 y Fh(32)p eop
1659 %%Page: 33 34
1660 33 33 bop 164 315 a Fd("Protein)29 b(Sequence)g(Alignments:)58
1661 b(A)30 b(Strategy)f(for)h(the)f(Hier-)164 376 y(archical)g(analysis)164
1662 436 y(of)h(residue)f(conservation")164 496 y(Computer)g(Applications)g
1663 (in)g(the)h(Biosciences,)164 556 y(9,)g(745-756.)949
1664 2607 y Fh(33)p eop
1665 %%Trailer
1666 end
1667 userdict /end-hook known{end-hook}if
1668 %%EOF