>> October 30, 1996

A new program, sc_to_e, can be used to calculate expectation values
from the regression coefficients reported from a search.  The
expectation value is based on similarity score, sequence length, and
database size.

>> November 8, 1996

fasta30t7 differs from fasta30t6 in the amount of information provided
with the -m 10 option.

(1) The query and library sequence identifiers are no longer abbreviated.

(2) New information about the program and program version are provided:

The new information provided is:

	mp_name: program name (actually argv[0])
	mp_ver: main program version (can be different from function version)
	mp_argv: command line arguments (duplicates argv[0])

    Some statistical information is provided as well:
	mp_extrap: XXXX YYY - statistics extrapolated from XXX to YYY
	mp_stats: indicates type of statistics used for E() value
	mp_KS: Kolmogorov-Smirnoff statistic

The "mp_" (main program) information is function independent, while the "pg_"
information is produced by a particular comparison function (ssearch,
fastx, fasta, etc).  "pg_" should probably be called "fn_", and "mp_"
called "pg_", but I remain backwards compatible.

(3) The end of the "parseable" records is denoted with:

	>>><<<

(4) There now an compile-time option -DM10_CONS, that allows you to
display a final alignment summary:

;al_cons:
     .::.:-   .:: ..  :.    .:.---:   :  .--.:. : 
..  .---  ..: :: ... :..: .::.:. .  .---.  .   .: 
 : .  . . :    ..   .    :..: .--. . : .:. .. :  .
 .:.:::  ..:. :

or, if M10_CONS_L is defined (in addition to M10_CONS), the output is:
;al_cons:
     p==p=-mmmp==mpzmm=pmmmmz=p---=mmm=mmp--p=zm=m
pzmmp---mmzp=m==mzzzm=zp=mz==z=pmzmmz---pmmpmmmp=m
m=mzmmzmpm=mmmmppmmmpmmmm=pp=mp--pmpm=mp=pmzzm=mmp
mp=z===mmpz=zm=

where '=' indicates identical residues, '-' a gap in one or the other
sequence, 'p' indicates a positive pam value, 'm' indicates a negative
pam value, and 'z' indicates a zero pam value.

A typical run now looks like:

>>>gtm1_mouse.aa, 217 aa vs s library
; mp_name: fasta3_t
; mp_ver: version 3.0t7 November, 1996
; mp_argv: fasta3_t -q -m 10 gtm1_mouse.aa s
; pg_name: FASTA
; pg_ver: 3.06 Sept, 1996
; pg_matrix: BL50
; pg_gap-pen: -12 -2
; pg_ktup: 2
; pg_optcut: 24
; pg_cgap: 36
; mp_extrap: 50000 51933
; mp_stats: Expectation fit: rho(ln(x))= 5.8855+/-0.000527; mu= 1.5386+/- 0.029;  mean_var=73.0398+/-15.283
; mp_KS: 0.0133 (N=29) at  42
>>GTM1_MOUSE GLUTATHIONE S-TRANSFERASE GT8.7 (EC 2.5.1.18) (GST 1-1) (CLASS-MU).
; fa_initn: 1490
; fa_init1: 1490
; fa_opt: 1490
; fa_z-score: 1754.6
; fa_expect:      0
; sw_score: 1490
; sw_ident: 1.000
; sw_overlap: 217
>GTM1_MOUSE ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKF
KLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVE
NQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS
RYIATPIFSKMAHWSNK
>GTM1_MOUSE ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKF
KLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVE
NQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS
RYIATPIFSKMAHWSNK
>>GTM1_RAT GLUTATHIONE S-TRANSFERASE YB1 (EC 2.5.1.18) (CHAIN 3) (CLASS-MU).
; fa_initn: 1406
; fa_init1: 1406
; fa_opt: 1406
; fa_z-score: 1656.3
; fa_expect:      0
; sw_score: 1406
; sw_ident: 0.931
; sw_overlap: 217
>GTM1_MOUSE ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKF
KLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVE
NQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS
RYIATPIFSKMAHWSNK
>GTM1_RAT ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRLLLEYTDSSYEEKRYAMGDAPDYDRSQWLNEKF
KLGLDFPNLPYLIDGSRKITQSNAIMRYLARKHHLCGETEEERIRADIVE
NQVMDNRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYHIFEPKCLDAFPNLKDFLARFEGLKKISAYMKSS
RYLSTPIFSKLAQWSNK
;al_cons:
:::::::::::::::::.:::::::::.::::.::::::.::::::::::
::::::::::::::::.::::::::.::::::::: ::::::::::::::
:::::.::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::..::::::::::::.:::::::::::::::::::
::..::::::.:.::::
>>><<<


217 residues in 1 query   sequences
18531385 residues in 52205 library sequences
 Tcomplib (4 proc)[version 3.0t7 November, 1996]
 start: Fri Nov  8 18:20:26 1996 done: Fri Nov  8 18:20:41 1996
 Scan time: 38.434 Display time:  2.166

Function used was  FASTA 

================================================================

>> November 11, 1996

 --> v30t71

Made changes to complib.c, comp_thr.c, nxgetaa.c to allow scoring
matrix to be modified in fastx3, fastx3_t.

================================================================

>> November 15, 1996

 --> v30t72

nxgetaa.c now accepts query sequences from "stdin" by using "-" as the
input file name.  If DNA sequences are read in this mode, the "-n"
option must be used.

> November 23, 1996

Included code in nxgetaa.c and Makefile.sgi to get around a bug in SGI's
sscanf() that prevented compressed GCG databases from being read properly.