readme.v34t0

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

(This searches swissprot for 2 iterations ("-j 2" using a E()
threshold 1e-6 saving the resulting position specific frequencies in
query.ckpt.  Note that the original query.fa and query.ckpt must
match.)

>>June 5, 2003

Fix to mshowbest.c to get -m 9 coordinates correct on reverse strand
with pv34comp*.  Some additional fixes for prfx34.

>>May 22, 2003

Changes to llgetaa.c, getseq.c, comp_lib.c to provide a different
library residue lookup table (sascii) for queries and libraries.  This
allows one to make a prfx34 (like prss34, but using the fastx
algorithm).  prfx34 is now available.

>>May 13,14 2003

Fixes to most of the drop*.c files, and mshowbest.c, to ensure that
coordinates displayed with -m 9(c) and the final alignment are
consistent.  They were consistent for fasta34/ssearch34/fasts34, but
not for fastx34/fasty34.  The alignment coordinate system has been
been revised for consistency in allthe drop*.c programs (coordinates
used to be off-by-one for some, but not other functions).

Fixes to -m 9c for fasty34/pv34compfy.  In addition, a problem was
fixed with fastx34/fasty34 that appeared with a protein sequence was
considerably longer than the DNA query, e.g. an EST vs titin (26K
residues).  This problem only appeared on pv34compfx/fy on Xserve's
under OS_X; but it should improve fastx34/fasty34 performance with
very long protein sequences on all platforms.

>>May 7,8 2003

Changes to p2_workcomp.c, compacc.c, and p_mw.h to fix persistent
bugs in the -m 9c display.  Previous pv34comp* programs would not
return the correct coded alignment if more than 100 alignments came
from the same node, or if an encoding was longer than 127 chars.

Also, fixes to p2_complib.c, comp_lib.c, to allow long query sequences
to be segmented.  Previously, only the first 20,000 residues were
used.  The segmented queries are not overlapped; segmented library
sequences are.

>>May 5, 2003

Changes to last_tat.c, scaleswt.c to ensure that all fasts alignments
that are likely to have significant scores are displayed.  In previous
implementations, if the query had more than 10 fragments, only the 100
best scores were shown.  Now, we rescore up to 2500 alignments.  The
new approach allows large mixtures to be used for searches, where some
of the fragments from the mixture match too many proteins
(e.g. actins).  Some differences between the fasts34 and pv34compfs
implementations have been fixed.  The two programs typically will not
give exactly the same results, because of small differences in the
sampling procedures, but the results are essentially equivalent.

>>Apr 11, 2003  CVS fa34t21b3

Fixes for "-E" and "-F" with ssearch34, which was inadvertantly disabled.

A new option, "-t t", is available to specify that all the protein
sequences have implicit termination codons "*" at the end.  Thus, all
protein sequences are one residue longer, and full length matches are
extended one extra residue and get a higher score.  For
fastx34/tfastx34, this helps extend alignments to the very end in
cases where there may be a mismatch at the C-terminal residues.

-m 9c has also been modified to indicate locations of termination
codons ( *1).

>>Mar 17, 2003  CVS fa34t21b2

A new option on scoring matrices "-MS" (e.g. "BL50-MS") can be used to
turn the I/L, K/Q identities on or off.  Thus, to make "fastm34" use
the isobaric identities, use "-s M20-MS".  To turn them off for "fasts34",
use "-s M20".

More fixes for correct alignment coordinates.  There was a conflict between
-m 9 and -m 9c and subsequent alignment displays.

>>Mar 13, 2003	

Various fixes to produce correct fastm34 alignments.  Changes to all
functions to correct potential problem with -m 9 alignment coordinates
when both -m 9 and actual alignments are shown.

>>Feb 25,27, 2003

Modifications to re-activate showsum.c, which included corrections to
the showbest() call in p2_complib.c.

>>Feb 13, 2003	CVS fa34t21b1

Modifications to dropfx.c to dramatically improve alignment speed for
cases where the DNA sequence is considerably longer than the protein
sequence.  Previously, a 200 aa vs 5000 nt comparison would do a full
200 x 5000 Smith-Waterman alignment; with this modification, no more
than a 200 x 1200 (2x3x200) alignment is done.  This optimization has
not (yet) been applied to dropfz2.c (fasty/tfasty).

>>Feb 11, 2003

Small modifications to comp_lib.c, p2_complib.c, and nmgetlib.c to
pass openlib() a possibly old lmf_str.  This allows openlib() to
re-use memory mapped files.  closelib() no longer releases memory
mapped file buffers.  Under Linux, memory mapped file buffers were not
really released, so when comparing a set of sequences against nr, the
program could not mmap() the database after several searches.  This
will also speed up memory mapped multiple sequence searches.

>>Jan 28-31, 2003  CVS fa34t21b0

Fix another bug (all of v34t20) involved with overlapping long
sequences.  And another bug that occurred when using sampled
statistics, but appeared only on the SGI platform - thanks to Dmitri
Mikhailov.  Several other issues have been addressed based on more
instrumented runtime testing.

Fix an old (all v34) bug that caused problems with -z 11-16 (shuffled
sequence array was not allocated properly).  Fixed another bug with -z
6/16 when using threaded (_t) searches in fasta34_t.

Restructure statistical analysis functions (scaleswn.c, scaleswt.c) to
return the "final" statistical estimation routine done in pst.zsflag_f.
This allows the program to cope with searches against a single sequence
correctly.

Corrected an error for DNA sequences needing Altschul-Gish statistics.

>>Jan 25, 2003

Add option "-J start:stop" to pv34comp*/mp34comp*.  "-J x" used to
allow one to start at query sequence "x"; now both start and stop can
be specified.

>>Jan 14, 2003

Changes to apam.c to provide an error message on stderr when a scoring
matrix cannot be found.

Changes to dropfs2.c, initsw.c, initfa.c to provide -m9c information
for fasts34 searches.  Modify the alignment algorithm to use
probabilistic scores properly.

>>Dec 22, 2002

Change to compacc.c (sortbeste()) to do a second sort on zscore when
several sequences have E() == 0.

>>Nov 27, 2002

Change FSEEK_T to fseek_t to keep Borland BCC5 happy. 

>>Nov 14-22, 2002  CVS fa34t20b6

Include compile-time define (-DPGM_DOC) that causes all the fasta
programs to provide the same command line echo that is provided by the
PVM and MPI parallel programs.  Thus, if you run the program:

    fasta34_t -q -S gtt1_drome.aa /slib/swissprot 12

the first lines of output from FASTA will be:

    # fasta34_t -q gtt1_drome.aa /slib/swissprot
     FASTA searches a protein or DNA sequence data bank
     version 3.4t20 Nov 10, 2002
    Please cite:
     W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

This has been turned on by default in most FASTA Makefiles.  

Fix p2_complib.c so that qstats[] is always allocated before it is used.

Fix serious bug in non-threaded comp_lib.c that caused some high
scoring sequences to be missed by fasts34.  New tests are included in
test.sh to detect this problem in the future.

The shell sort algorithm in sortbeste(), sortbestz(), and sortbesto()
has been modified to use an improved algorithm that will not go
quadratic in pathological cases.

nmgetlib.c and mmgetaa.c have been modified to remove "^A" in libstr
when used with p2_complib.c.

Fix problem with MAXSEG in tatstats.h with IBM/AIX.

Changes to most Makefiles to use -DSAMP_STATS; fixes to p2_complib.c
for SAMP_STATS.

>>Oct 22, Nov 3, Nov 9, 2002   CVS tag fa34t20b5

Fix problem in comp_lib.c that caused the query sequence length to be
counted twice.

Fixed problem with prss34 (updated find_zp in showrss.c).

Correct shuffling function in several places.

Add jitter back to addhistz() - improves appearance with prss34.

Changes to fix problems with aln_code using -m 9c.

Fix to serious bug in scaleswt.c (fasts34, etc) that caused sorts on
the high scores to take much to long.  The program is now 10X faster,
and scales well on PVM/MPI.

Fix to llgetaa.c to work with new getseq() API with automatic alphabet
recognition.

>>Oct 12, 2002 CVS tag fa34t20b4

Several very obscure (and sometimes old) bugs that appeared in certain
MPI environments have been fixed.  This occurred because the pst.sq[]
array did not always have a '\0' at the end.  In addition,
mshowalign.c/p2_workcomp.c sometimes failed to put the '\0' at the end
of seqc0/seqc1.  Correct bug introduced in fa34t20b3 for fasts34(_t).

>>Oct 9, 2002 CVS tag fa34t20b3

Fix to apam.c build_xascii() to not zero-out qascii[0].  Fix
Makefile.pvm4.  Mix problem with -m 9c with compacc.c.

>>Sept 28, 2002 

Additional fixes to -m 9c in p2_complib.c/compacc.c/mshowbest.c.
Remove restriction in fasts34(_t) to less than 30 peptides (though no
more than 30 peptides can be aligned currently).

>>Sept 24, 2002

Fix p2_workcomp.c so that e_scores are delivered correctly when
last_calc flag is set, and -m 9c provides alignments when only one
best hit is present.

Fix comp_lib.c to use different maxn and overlap for each different
query sequence.  fasta34 and fasta34_t now have identical results when
a long sequence is searched.

Add '@C:101' support to memory mapped FASTA format files.

Fix mshowalign.c so that coordinates returned by cal_coord() use
loffset+l_off.

>>Sept 14, 2002	CVS tag fa34t20b2

Changes to p2_complib.c, compacc.c to fix statistics problems with
pv34compfs on query sequences with more than 10 fragments.

>>Aug 27, 2002

Modifications to mshowbest.c and drop*.c (and p2_workcomp.c,
compacc.c, doinit.c, etc.) to provide more information about the
alignment with the -m 9 option.  There is now a "-m 9c" option, which
displays an encoded alignment after the -m 9 alignment information.
The encoding is a string of the form: "=#mat+#ins=#mat-#del=#mat".
Thus, an alignment over 218 amino acids with no gaps (not necessarily
100% identical) would be =218.  The alignment:

       10        20        30        40        50          60         70  
GT8.7  NVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLDFPNLPYL-IDGSHKITQ
       :.::  . :: ::  .   .:::         : .:    ::.:   .: : ..:.. :::  :..:
XURTG  NARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLMFDQVPMVEIDG-MKLAQ
               20        30                 40        50        60        

would be encoded: "=23+9=13-2=10-1=3+1=5".  The alignment encoding is
with respect to the beginning of the alignment, not the beginning of
either sequence.  The beginning of the alignment in either sequence is
given by the an0/an1 values. This capability is particularly useful
for [t]fast[xy], where it can be used to indicate frameshift positions
"/#\#" compactly.  If "-m 9c" is used, the "The best scores" title
line includes "aln_code".

>>Aug 14, 2002	CVS tag fa34t20

Changes to nmgetlib.c to allow multiple query searches coming from
STDIN, either through pipes or input redirection.  Thus, the command

       cat prot_test.lseg | fasta34 -q -S @ /seqlib/swissprot

produces 11 searches.  If you use the multiple query functions, the
query subset applies only to the first sequence.

Unfortunately, it is not possible to search against a STDIN library,
because the FASTA programs do not keep the entire library in memory
and need to be able to re-read high-scoring library sequences.  Since
it is not possible to fseek() against STDIN, searching against a STDIN
library is not possible.

>>Aug 5, 2002

fasts34(_t) and fastm34(_t) have been modified to allow searches with
DNA sequences.  This gives a new capability to search for DNA motifs,
or to search for ordered or unordered DNA sequences spaced at
arbitrary distances.

>>Aug 4, 2002

comp_lib.c has been modified to provide comp_mlib.c function.
comp_mlib.c is no longer used.  comp_lib.c with the "mlib" function
can now recognize protein or DNA sequences automatically, and reads
from stdin can now detect DNA/protein sequence types automatically.
Changes to compacc.c, getseq.c, doinit.c initfa.c, initsw.c, and
nmgetlib.c to support automatic sequence type detection.

>>July 28-31, 2002

(1) The various Makefile's have been "normalized".  The fast*34[_t]
    (Makefile.34m.common[_sql]), Makefile.pvm4[_sql], and
    Makefile.mpi4[_sql] make files all use a common set of filenames,
    described in Makefile.fcom.  This greatly simplifies adding
    programs, but requires that all *.o files be deleted when moving
    from fast*34* to pv34comp* to mp34comp*.

(2) showalign.c/p_showalign.c have been merged into mshowalign.c
    showbest.c/manshowbest.c have been merged into mshowbest.c.  Some
    of the related files (showun.c, manshowun.c, have not been merged
    or tested).

(3) Code for ranking scores with valid e_value's incorporated.

(4) Bug fixes in p2_complib.c, so that fasts34/fasts34_t/pvcompfs
    provide identical statistics.

>>July 26, 2002

Makefile.pvm4_sql and Makefile.pvm4 have been substantially simplified
by providing the worker program name from the h_init() function in the
initfa.c/initsw.c files.

>>July 24, 2002

Substantial modifications to param.h, structs.h to ensure that no
sequence specific information is kept in struct pstruct.  This
structure now holds the pam[] matrix, and other scoring parameters,