readme.v34t0

序列对齐 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequenc

Changes to comp_lib.c (and Makefile.pcom) to support prss34_t.

>>Feb 12, 2005

Modify dropfs.c to dynamically allocate space for alignments, so that
queries with a large number of fragments can still place all the
fragments on the alignment.  Also fix a problem produced by removing
-DBIGMEM from most of the Makefile's, but not fixing defs.h to use
BIGMEM sizes by default.

>>Jan 24, 2005

Include a new program, "print_pssm", which reads a blastpgp binary
checkpoint file and writes out the frequency values as text.  These
values can be used with a new option with ssearch34(_t) and prss34,
which provides the ability to read a text PSSM file.  To specify a
text PSSM, use the option -P "query.ckpt 1" where the "1" indicates a
text, rather than a binary checkpoint file.  "initfa.c" has also been
modified to work with PSSM files with zero's in the in the frequency
table.  Presumably these positions (at the ends) do not provide
information. (Jan 26, 2005) blastpgp actually uses BLOSUM62 values
when zero frequencies are provided, so read_pssm() has been modified
to use scoring matrix values for zero frequencies as well.

>>Jan 13, 2005

Change to initfa.c to have fasts34 do a protein comparison by default,
rather than an unknown sequence type.  Automatic checking for fasts34
does not work reliably, because queries can be very short.  Likewise
for fastm34.  [Jan 26, 2004] Undo this change, which broke DNA
comparison when "-n" was specified.

>>Jan 7, 2005

Changes to tatstats.h, dropfs2.c to allow larger numbers of peptides
to match when fasts is used to show coverage on a proteomics
experiment.  Previously fasts could match no more than 30 peptides,
that has been increased to 50.  In addition, ktup=2 can be used
to increase the likelihood that short exact matchs trump longer
mismatched regions.  

>>Nov 11, 2004	   CVS fa34t25

Finished merge of earlier fa34t24 branch with HEAD.  Correct
labeling of TFASTM.

>>Nov 4-8, 2004	   

Incorporation of Erik Lindahl "anti-diagonal" Altivec code for
Smith-Waterman, only.  Altivec SSEARCH is now faster than FASTA for
query sequences < 250 amino acids.

Small modifications to output score display to ensure that the correct
scores are shown, and that they are correctly labeled.

>>Aug 25,26, 2004  CVS fa34t24b3

Small change in output format for p34comp* programs in
">>>query_file#1 string" line before alignments.  This line is not present
in the non-parallel versions - it would be better for them to be consistent.

Change in last_stats.c to properly label fasts statistics with -z != 1.

Change in dropfs2.c to ensure that tatprobs are not precalculated with -z 4.

Modify -m 9i output option to show in HTML output.

Add "#ifdef NOOVERHANG" to dropfs2.c that causes overlapping
alignments to score a 0, rather than the partial overlap score.
Useful for SAGE alignments, because "fasts" requires global alignments
(except for for overhangs, unless NOOVERHANG is defined).

>>Aug 23, 2004

Fix problem with very long definition lines with formatdb version4
ASN databases.  Fix mshowalign.c to re-enable "-L" option.

>>July 28, 2004 

Fix to re-enable -w window shuffle for PRSS.  Modify comp_lib.c
for PRSS to ensure that the unshuffled score and probability
are shown, even for very high probabililty alignments.

>>July 21, 2004

Modifications to support PostgreSQL databases with the same commands
as MySQL databases.  MySQL database libraries are type 16, PostgreSQL
are type 17.  Makefile.linux_sql and Makefile.pvm4_sql support both
database types simultaneously.

>>June 23, 2004 CVS fa34t24b2

Additional fixes to enable -n or -p with fasts34 and
fastm34. Makefile.pcom was fixed for fastm34_t.  A new file,
mgstm1.nts, of DNA fragments from mgstm1.seq, is included for testing
fasts34 and fastm34.

>>May 4, 2004  

Fixes to initfa.c to allow DNA:DNA for FASTS, FASTM.  This change
introduced a bug that broke FASTS completely, but was fixed June 18,
2004 (and retagged fa34t24b2).

>>April 23, 2004 CVS fa34t24b1

Fix bug in initfa.c that caused tfasts/tfastf not to examine all six
frames.

>>May 4, 2004

Fixes to initfa.c to allow DNA:DNA for FASTS, FASTM.

>>March 19, 2004 CVS fa34t24b0

Modify all the drop*.c files, plus mshowbest.c and mshowalign.c, to
display percent similarity, rather than percent ungapped.  An
alignment is counted as similar if the score is greater than or equal
to zero (the same criterion used for placing ".". To disable this
change, remove -DSHOWSIM from the appropriate Makefile.*.

>>March 18, 2004 CVS fa34t23b8

Fix bug in initfa.c tables that caused prss to generally compare
proteins.

>>March 15, 2004 

Fix bug in calls to revcomp(); make revcomp() guarantee NULL termination.

>>March 2, 2004	CVS fa34t23b7

Fix a very embarrassing and surprising bug that caused insertions
in fasta alignments to appear in the wrong sequence.

>>Feb 7, 2004	CVS fa34t23b6

Change initfa.c to allow "-i" (reverse complement) and "-i -3" with
"fastx34" and "prfx34".  In addition, "prfx34" now examines both query
DNA strands in calculated the shuffled statistical significance.

>>Feb 5, 2004

Reverse assignments for G:U baseparing in initfa.c.

Fix memory allocation error caused by doubling DNA alignment width.

>>Jan 7, 2004	CVS fa34t23b5

Change in do_walign() in dropnfa.c to make final DNA alignments use a
band that is 2X as large as the search band width.

>>Dec 22, 2003	CVS fa34t23b4

Fix typo in p2_complib.c that prevented compilation.  Fix problem
with karlin.c for asymmetrical matrices, such as used with -U.

>>Dec 10, 2003  CVS fa34t23b3

Fix problem in resetp()/initfa.c that disabled banded Smith-Waterman
DNA alignments.

Allow spam() to do extended alignments for DNA if one of the sequences
is < 50 nt.

Cause default ktup to drop for short sequences.  For protein < 50, ktup=1;
for DNA < 20, 50, 100 ktup = 1, 2, 3, respectively.

>>Dec 7, 2003

A new option, "-U" is available for RNA sequence comparison.  "-U"
functions like "-n", indicating that the query is an RNA sequence.  In
addition, to account for "G:U" base pairs, "-U" modifies the scoring
matrices so that a "G:A" match has the same score as a "G:G" match,
and "T:C" match has the same score as a "T:T" match.  The asymmetric
matrix required changes in dropnfa.c that were similar to the changes
in dropgsw.c required for profiles.  In addition, m_msg.qdnaseq and pst.dnaseq
 can now be SEQT_DNA, SEQT_RNA, SEQT_PROT, SEQT_UNK, or SEQT_OTHER.
m_msg.ldnaseq does not use SEQT_RNA, only SEQT_DNA.  A new member of
struct pstruct: int nt_align, is used to indicate nucleotide
alignments.

>>Nov 19, 2003

Changes to Makefile's to distinguish between tatstats_fs.o and
tatstats_ff.o.

>>Nov 2, 2003

Substantial changes to comp_lib.c, p2_complib.c, mshowbest.c, and
mshowalign.c to support more sophisticated display options.
Previously, one could have only on "-m #" option, even though several
of the options were orthogonal (-m 9c is independent of -m 1 and -m2,
which is independent of -m 6 (HTML)).  The programs now use a bitmask
that allows independent options to be combined.  In particular -m 9c
can be combined with -m 6, which can be very helpful for runs that
need HTML output but can also exploit the encoding provided by -m 9c.

The "-m 9" option now also allows "-m 9i", which shows the standard
best score information, plus percent identity and alignment length.

>>Oct 26, 2003	CVS fa34t23b1

Additional fixes to Makefiles to enable tfastf34(_t).  Changes to
support ossearch34 (a non-Phil Green optimized Smith-Waterman).

>>Oct 8, 2003	CVS fa34t23b0

Fixes to get DNA queries working in both directions, and to fix PCOMPLIB
programs for "-V" option.  Currently, the parallel programs cannot use
the "-V" option.

>>Sept 25, 2003

A new option is available for annotating alignments.  -V '@#?!'
can be used to annotate sites in a sequence, e.g:
	>GTM1_HUMAN ...
	PMILGYWDIRGLAHAIRLLLEYTDS@S?YEEKKYT@MG
	DAPDYDRS@QWLNEKFKLGLDFPNLPYLIDGAHKIT
might mark known and expected (S,T) phosphorylation sites.  These
symbols are then displayed on the query coordinate line:

               10        20    @?  30  @     40  @     50        60
GTM1_H PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLP
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
gtm1_h PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLP
               10        20        30        40        50        60

This annotation is mostly designed to display post-translational
modifications detected by MassSpec with FASTS, but is also available
with FASTA and SSEARCH.

>>Sept 22, 2003	  CVS fa34t22b5

The Altivec Smith-Waterman code has been removed.

>>Sept 17, 2003	  CVS fa34t22b4

A variety of different bugs have been fixed.  (1) All the functions in
the old initsw.c are now in initfa.c; initsw.c will be removed.
Specifically, the Profile/PSSM code is now in initfa.c.  initfa.c is
now fully table driven. (2) various problems with prss34 and prfx34
have been fixed in initfa.c.  (3) An additional ncbl2_mlib.c buffer
overrun has been fixed. (4) fastf34 is now available in this package.
Its performance is very similar to, but not identical to, fastf33.  I
am tracking down the differences.  In general, the raw scores
calculated by both programs are the same, but the statistical analysis
seems to be slightly different.

>>July 30, 2003   CVS fa34t22b3

Fix bug in ncbl2_mlib.c that caused buffer overrun with blast/formatdb
v3 description lines.

>>July 28, 2003

The initfa.c file has been substantially re-structured to use a
table-driven approach to parameter setting, rather than the previous
confusing combinations of #ifdef's.  Two tables of parameters are
used, pgm_def_arr[] and msg_def_arr[], which specify values like the
program name, reference, scoring matrix, default gap penalties, etc.
msg_def_arr[] has the sequence types for the query, library, and
algorithm, as well as other parameters (qframe, nframe, nrelv, etc),
which greatly simplifies the sequence recognition logic.  ppst->pgm_id
can be used to identify the program that is running.  Eventually,
almost all of the program specific #ifdef's will be removed from
initfa.c.  initfa.c now provides initsw.c functionality, so that
initsw.c is no longer needed.

>>July 25, 2003

A new file is included - fasta.defaults - that lists the scoring
matrix, gap penalty, and other defaults for all of the fasta34
programs.  This file will be used soon to simplify parameter setting
for the FASTA programs, and should also be used by Javascript WWW
interfaces to the FASTA programs.

>>July 22, 2003    CVS fa34t22b2

Fixes to dropfs2.c, tatprobs.c to ensure that negative probabilities
cannot occur.  Negative probabilities were never seen with standard
matrices, but did occur with BL50.  Another optimization in dropfs.c
considerably improves fasts34 performance in some cases.

Fix a problem with formatdb v4 ASN.1 format files.

>>July 12, 2003

Fix a bug that prevented "-L" (long sequence descriptions) from
working.

>>July 9, 2003

Fix reverse complement (M:K) error.  Fix off-by-one error for FASTA
DNA alignments that caused the first aligned residue pair to be
missed.

>>July 4 - 8, 2003

Incorporate blast-def-line ASN.1 parsing so that NCBI formatdb version
4 files can be read.

>>June 26, 2003

The strategy for displaying the match/mismatch line (" .:" for -m 0)
has been changed dramatically to acommodate more sophisticated
strategies for indicating conservative replacements, e.g. because of
PSSM's.  In addition to seqc0 and seqc1, which hold the aligned
sequences for display, there is also seqca, which holds the alignment
symbol.  calcons(), do_show(), and discons() have all changed to
include seqca.  calcons() is somewhat more complex; discons() is much
simpler.  (June 29, 2003 - dropgsw.c calcons() now displays profile
similarity accurately - it is very very illuminating.)

>>June 16, 2003	version: fasta34t22

ssearch34 now supports PSI-BLAST PSSM/profiles.  Currently, it only
supports the "checkpoint" file produced by blastall, and only on
certain architectures where byte-reordering is unnecessary.  It has not
been tested extensively with the -S option.

	ssearch34 -P blast.ckpt -f -11 -g -1 -s BL62 query.aa library

Will use the frequency information in the blast.chkpt file to do a
position specific scoring matrix (PSSM) search using the
Smith-Waterman algorithm.  Because ssearch34 calculates scores for
each of the sequences in the database, we anticipate that PSSM
ssearch34 statistics will be more reliable than PSI-Blast statistics.

The Blast checkpoint file is mostly double precision frequency
numbers, which are represented in a machine specific way.  Thus, you
must generate the checkpoint file on the same machine that you run
ssearch34 or prss34 -P query.ckpt.  To generate a checkpoint file,
run:

blastpgp -j 2 -h 1e-6 -i query.fa -d swissprot -C query.ckpt -o /dev/null