fasta32t05 release

William R. Pearson wrp at alpha0.bioch.virginia.edu
Thu May 13 10:54:18 EST 1999

A new version of the fasta program package is available from:


This version fixes some serious bugs in the fastx3 alignment function,
and provides more informative alignment coordinates with the alignment
output.  As a result of the alignment numbering, several other alignment
numbering bugs were found and fixed.

The recent revision history is shown below.

Bill Pearson


>>May 12, 1999
 --> v32t05

Fixed a serious bug in the fastx3/tfastx3 alignment display which
caused t/fastx3 to produce incorrect alignments (and incorrectly low
percent identities).  The scores were correct, but the alignment
percent identities were too low and the alignments were wrong.

Numbering errors were also corrected in fastx3/tfastx3 and
fasty3/tfasty3 and when partial query sequences were used.

>>May 7, 1999

Fixed a subtle bug in dropgsw.c that caused do_work() to calculate
incorrect Smith-Waterman scores after do_walign() had been called.
This affected only pvcompsw searches with the "-m 9" option.

>>May 5, 1999

Modified showalign.c to provide improved alignment information that
includes explicitly the boundaries of the alignment.  Default
alignments now say:

Smith-Waterman score: 175;  24.645% identity in 211 aa overlap (5-207:7-207)

>>May 3, 1999

Modified nxgetaa.c, showsum.c, showbest.c, manshowun.c to allow a
"not" superfamily annotation for the query sequence only.  The
goal is to be able to specify that certain superfamily numbers be
ignored in some of the search summaries.  Thus, a description line
of the form:

>GT8.7 | 40001 ! 90043 | transl. of pa875.con, 19 to 675

says that GT8.7 belongs to superfamily 40001, but any library
sequences with superfamily number 90043 should be ignored in any
listing or summary of best scores.

In addition, it is now possible to make a fasta3r/prcompfa, which is
the converse of fasta3u/pucompfa. fasta3u reports the highest scoring
unrelated sequences in a search using the superfamily annotation.
fasta3r shows only the scores of related sequences.  This might be
used in combination with the -F e_val option to show the scores
obtained by the most distantly related members of a family.

>>April 25, 1999

 -->v32t04 (not distributed)

Modified nxgetaa.c to remove the dependence of tgetaa.o on TFASTA
(necessary for a more rational Makefile structure).  No code changes.

>>April 19, 1999

Fixed a bug in showalign.c that displayed incorrect alignment coordinates.
(no version number change).

>>April 17, 1999

 --> v32t03

A serious bug in DNA alignments when the sequence has been broken into
multiple segments that was introduced in version fasta32 has been
fixed.  In addition, several minor problems with -z 3 statistics on
DNA sequences were fixed.

Added -m 9 option, which unfortunately does different things in
pvcompfa/sw and fasta3/ssearch3.  In both programs, -m 9 provides the
id's of the two sequences, length, E(), %_ident, and start and end of
the alignment in both sequences.  pvcompfa/sw provides this
information with the list of high scoring sequences.  fasta3/ssearch3
provides the information in lieu of an alignment.

>>March 18, 1999

 --> v32t02

Added information on the algorithm/parameter description line to
report the range of the pam matrices.  Useful for matrices like
MD_10, _20, and _40 which require much higher gap penalties.

>>March 13, 1999 (not distributed)

 --> v32t01 

 -r results.file  has been changed to -R results.file to accomodate
 DNA match/mismatch penalties of the form: -r "+1/-3".

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