+++ /dev/null
->> 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.
-
git://source.jalview.org / jabaws.git / blobdiff