readme.v35

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

 $Name: fa35_03_06 $ - $Id: readme.v35,v 1.29 2008/04/02 14:59:09 wrp Exp $

>>Apr. 2, 2008

Ensure that code in last_init() to modify ktup never increase ktup value.

>>Mar. 4, 2008

Fix parsing of parameters (matrix, gap open, gap ext) in ASN.1 PSSM
files produced by blastpgp.

>>Feb. 18, 2008	  fa35_03_05

Re-implement -M low-high sequence range options.  Sequence range
restriction has probably been missing since the introduction of
ggsearch and glsearch, which use a new approach to limiting the
sequence range.

>>Jan. 25, 2008	   fa35_03_04

Map 'O' (pyrrolysine) to 'K', 'U' (seleno-cysteine) to 'C' in uascii.h
('J' is already recognized and mapped to the average of 'I' and 'L').
Thus, 'J' will appear in alignments, but 'O' and 'U' are transformed
to 'K' and 'C'.

Because "Oo" and "Uo" are not (currently) part of aax[] ("Uu" is in
ntx[]), apam.c/build_xascii() was extended to add characters from
othx[] - "oth" for "other" so that they are not lost.

Double check, and fix, some mappings for 'J/j' and 'Z/z'.

>>Jan. 11, 2008	   fa35_03_03

Clean up some issues with -m 10 output; put "; mp_Algorithm", ";
mp_Parameters" down with other -m 10 ";" lines.  Also provide ";
al_code" and "; al_code_ann" if -m 9c is specified.  Remove duplicate
">>>query" line.

Add "; aln_code" and "; ann_code" to -m 10 -m 9c output.  The
alignment/annotation encoding is only produced once (in showbest(),
and is then saved for -m 10 aligment.

>>Dec. 13, 2007	  fa35_03_02m (merge of fa35_03_02 and fa35_02_08_br)

Add ability to search a subset of a library using a file name and a
list of accession/gi numbers. This version introduces a new filetype,
10, which consists of a first line with a target filename, format, and
accession number format-type, and optionally the accession number
format in the database, followed by a list of accession numbers.  For
example:

	  </slib2/blast/swissprot.lseg 0:2 4|
	  3121763
	  51701705
	  7404340
	  74735515
	  ...

Tells the program that the target database is swissprot.lseg, which is
in FASTA (library type 0) format.

The accession format comes after the ":".  Currently, there are four
accession formats, two that require ordered accessions (:1, :2), and
two that hash the accessions (:3, :4) so they do not need to be
ordered.  The number and character after the accession format
(e.g. "4|") indicate the offset of the beginning of the accession and
the character that terminates the accession.  Thus, in the typical
NCBI Fasta definition line:

 >gi|1170095|sp|P46419|GSTM1_DERPT Glutathione S-transferase (GST class-mu)

The offset is 4 and the termination character is '|'.  For databases
distributed in FASTA format from the European Bioinformatics
Institute, the offset depends on the name of the database, e.g.
	   
 >SW:104K_THEAN Q4U9M9 104 kDa microneme/rhoptry antigen precursor (p104).

and the delimiter is ' ' (space, the default).

Accession formats 1 and 3 expect strings; accession formats 2 and 4
work with integers (e.g. gi numbers).

>>Dec. 12, 2007  fa35_02_08

Correct bug in ssearch35 gapped scores that only occurred in
non-accelerated code.  This bug has been present since fa35_02_06.
Modified the Makefiles so that accelerated (ssearch35(_t)) and
non-accelerated (ssearch35s(_t)) are available. Edited Makefile's to
provide accelerated ssearch35 more specifically.

Modifications to provide information about annotated residues in the
-m9c coded output. Previously, -m 9c output added a field:

    =26+9=15-2=9-1=3+1=74-2=3-3=63

after the standard -m 9 output information.  With the new version, an
annotated query sequence ( -V '*#' ) adds the field:

    |14:16:#<TM|24:26:#>TA|44:37:*>ST|71:66:#=TT

which indicates that residue 14 in the query sequence aligns with
residue 16 in the target (library) with annotation symbol '#', the
alignment score is '<' less than zero, and the residues are 'T'
(query) and 'M' (library). (The '|' is used to separate each
annotation entry.)

>>Nov. 10, 2007

Parts of p2_complib.c and p2_workcomp.c, and the pvm/mpi Makefiles,
have been updated to be consistent with name changes in the param.h
and structs.h directories.

>>Nov. 20, 2007   fa35_02_08

Parts of p2_complib.c and p2_workcomp.c, and the pvm/mpi Makefiles,
have been updated to be consistent with name changes in the param.h
and structs.h directories.

>>Nov. 6, 2007	  fa35_02_07

Correct problems with asymmetric RNA matrices in initfa.c and rna.mat.

>>Oct. 18, 2007

Correct problem parsing ASN1 FastaDefLines when the database is local.

Recovering from a misplaced cvs commit of code that was supposed to be
on a branch, code has been recovered from earlier versions (fa35_02_05
because fa35_02_06 has some branch contamination).

>>Oct. 4, 2007	  fa35_02_06

Correct error in gap penalties in dropnnw.c.  Due to an unfortunate
inconsistency, the gap parameter in FLOCAL_ALIGN (in dropgsw2.c) had a
different meaning than that in almost all the other programs (it was
the sum of gap_open and gap_ext).  The FLOCAL_ALIGN function call was
copied for FGLOBAL_ALIGN, even though the the FGLOBAL_ALIGN function
used the more conventional gap_open, gap_ext parameters.  Thus,
FGLOBAL_ALIGN was wrong and the subsequent do_walign() in dropnnw.c
were wrong.  dropgsw2.c:FLOCAL_ALIGN has been modified to use the
conventional gap_open parameter, and calls to dropnnw.c:
FGLOBAL_ALIGN() and do_walign() have been fixed.

>>Sept. 20, 2007

Modify the logic used when saving a seq_record *seq_p into beststr
*bbp to ensure that if the seq_record is replaced, it is replaced at
all the places where it is referenced.  This involves adding a linked
list into beststr (*bbp->bbp_link).  When making the link (and freeing
it up), be certain that the linked seq_p is the same as the one being
replaced.

>>Sept. 18, 2007   fa35_02_05

A relatively obscure problem was found on the SGI platform when
searching a library smaller than 500 sequences (thus requiring some
shuffles). Two bugs were found and corrected; one involved not
allocating aa1shuff with COMP_THR and not do a m_file_p->ranliba()
before re_getlib().  The second involved destroying a pointer to the
list of seq_records when a sequence was being shuffled.  The bugs were
confirmed with Insure, and have been fixed.

>>Sept. 7, 2007	fa35_02_04

Revamp the offset handling code to provide better uniformity between
query and library offsets and coordinate systems.

Fix a problem with load_mmap() to load 64-bit sequence locations
properly on machines with 32-bit integers.

>>Sept. 4, 2007

Modify ncbl2_mlib.c slightly to check to see whether the amino-acid
mapping in blast databases is identical to the FASTA mapping (it
should be).  If they are identical, do not re-map the blast amino acid
sequences (potentially a small speed up).

>>Aug. 22, 2007

Change ps_lav.c to lav2ps.c, and add lav2svg.c.  It is now possible to
generate a lalign35 HTML output that has both SVG (lav2svg) and PNG
(lav2ps | gs ), graphics.

>>Aug. 10, 2007	CVS fa35_02_03

Fix faatran.c:aacmap() bug.

>>Aug. 6, 2007

Extensive restructuring of pssm_asn_subs.c to parse PSSM:2 ASN.1's
downloaded from NCBI WWW PSI-BLAST more robustly.

>>July 25, 2007	  CVS fa35_02_02

Change default gap penalties for OPTIMA5 matrix to -20/-2 from -24/-4.

>>July 24, 2007

Correct bugs introduced by adding 'J' - 'J' was initially put before
'X' and '*' in the alphabet, which led to problems because the
one-dimensional lower-triangular pam[] matrices (abl50[], abl62[],
etc) had entries for 'X', and '*', but not for 'J'.  By placing 'J'
after the other characters, the problem is resolved.

Modify tatstats.c to accommodate 'J'.