readme.v35

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

'*' is back in the aascii[] matrix, so that it is present by default
(like fasta34).

>>July 23, 2007

Changes to support sub-sequence ranges for "library" sequences -
necessary for fully functional prss (ssearch35) and lalign35.  For all
programs, it is now possible to specify a subset of both the query and
the library, e.g.

    lalign35 -q mchu.aa:1-74 mchu.aa:75-148

Note, however, that the subset range applied to the library will be
applied to every sequence in the library - not just the first - and
that the same subset range is applied to each sequence.  This probably
makes sense only if the library contains a single sequence (this is
also true for the query file).

Correct bugs in the functions that produce lav output from lalign35 -m
11 to properly report the begin and end coordinates of both sequences.
Previously, coordinates always began with "1".  Correct associated bug
in ps_lav.c that assumed coordinates started with "1".

>>June 29, 2007	CVS fa35_02_01

Merge of HEAD with fasta35 branch.

>>June 29, 2007	CVS fa35_01_06

Add exit(0); to ps_lav.c for 0 return code.

>>June 26, 2007

Add amino-acid 'J' for 'I' or 'L'.

Add Mueller and Vingron (2000) J. Comp. Biol. 7:761-776 VT160 matrix,
"-s VT160", and OPTIMA_5 (Kann et al. (2000) Proteins 41:498-503).

Changes to dropnnw.c documentation functions to remove #ifdef's from
strncpy() - which apparently is a macro in some versions of gcc.

>>June 7, 2007

Modify initfa.c to allow ggssearch35(_t), glsearch35(_t) to use PSSMs.

>>June 5, 2007  CVS fa35_01_05

Modifications to p2_complib.c, p2_workcomp.c to support Intel C
compiler.  Fixed bug in p2_workcomp.c - gstring[2][MAX_STR] required -
[MAX_SSTR] too short.  mp35comp* programs now tested and working (as
are pv35comp*, c35.work* programs).

Fix problem with fasts/fastm/fastf last_tat.c with limited memory.

Correct problem with lalign35.exe Makefile.nm_[fp]com.

Add $(CFLAGS) to map_db to enable large file support.

Address problem with PSSM's when '*' not defined (initfa.c:extend_pssm()).

>>May 30, 2007	CVS fa35_01_04

Complete work on ps_lav, which converts an lalign35 lav (-m 11) file
into a postscript plot, which looks identical to the plots produced by
plalign from fasta2.

>>May 25,29, 2007

Changes to defs.h, doinit.c mshowalign.c for -m 11, which produces lav
output only for lalign35.

Changes to comp_lib2.c to add m_msg.std_output, which provides all the
standard print lines.  This is turned off for -m 11 (lav) output.
lalign35 -m 11 provides standard lav output, with the addition of
#lalign35 -q ... .

>>May 18, 2007

Add m_msg.zsflag to preserve pst.zsflag when reset by global/global
exclusion of many library sequences.

>>May  9, 2007	CVS fa35_01_03

Tested local database size determination with p2_complib2/p2_workcomp2.

>>May 2, 2007	renamed fasta35, pv35comp, etc

Separate thread buffer structures from param.h.

Problems with incorrect alignments has been fixed by re-initializing the
best_seqs and lib_buf2_list.buf2 structures after each query sequence.

The labels on the alignment scores are much more informative (and more
diverse).   In the past, alignment scores looked like:

>>gi|121716|sp|P10649|GSTM1_MOUSE Glutathione S-transfer  (218 aa)
 s-w opt: 1497  Z-score: 1857.5  bits: 350.8 E(): 8.3e-97
Smith-Waterman score: 1497; 100.0% identity (100.0% similar) in 218 aa overlap (1-218:1-218)
^^^^^^^^^^^^^^

where the highlighted text was either: "Smith-Waterman" or "banded
Smith-Waterman". In fact, scores were calculated in other ways,
including global/local for fasts and fastf.  With the addition of
ggsearch35, glsearch35, and lalign35, there are many more ways to
calculate alignments: "Smith-Waterman" (ssearch and protein fasta),
"banded Smith-Waterman" (DNA fasta), "Waterman-Eggert",
"trans. Smith-Waterman", "global/local", "trans. global/local",
"global/global (N-W)".  The last option is a global global alignment,
but with the affine gap penalties used in the Smith-Waterman
algorithm.

>>April 24, 2007

The new program structure has been migrated to the PVM and MPI
versions.  In addition, the new global algorithms (pv35compgg,
pv35compgl) have been moved, though the the PVM/MPI versions do not
(yet) to the appropriate size filtering.

>>April 19, 2007

Two new programs, ggsearch35(_t) and glsearch35_t are now available.
ggsearch35(_t) calculates an alignment score that is global in the
query and global in the library; glsearch35_t calculates an alignment
that is global in the query and local, while local in the library
sequence.  The latter program is designed for global alignments to domains.

Both programs assume that scores are normally distributed.  This
appears to be an excellent approximation for ggsearch35 scores, but
the distribution is somewhat skewed for global/local (glsearch)
scores.  ggsearch35(_t) only compares the query to library sequences
that are beween 80% and 125% of the length of the query; glsearch
limits comparisons to library sequences that are longer than 80% of
the query.  Initial results suggest that there is relatively little
length dependence of scores over this range (scores go down
dramatically outside these ranges).

A bug was found and fixed in showalign() and showbest() where the
aa1save buffer was not preserved when some sequences needed to be
re-read, while others were stored in the beststr.

>>April 9, 2007

Some of the drop*.c functions have been reconfigured to reduce the
amount of duplicate code.  For example, dropgsw.c, dropnsw.c, and
dropnfa.c all used exactly the same code to produce global alignments
(NW_ALIGN() and nw_align()), this code is now in wm_align.c.
Likewise, those same files, as well as dropgw2.c, use identical code
to produce consensus alignments (calcons(), calcons_a(), calc_id(),
calc_code()).  Rather than working with three or four copies of
identical code, there is now one version.

>>March 29, 2007

At last, the lalign (SIM) algorithm has been moved from FASTA21 to
FASTA35.  Currently, only lalign35 is available.  A plotting version
will be available shortly (or perhaps a more general solution that
produces lav output).

The statistical estimates for lalign35 should be much more accurate
than those from the earlier lalign, because lambda and K are estimated
from shuffles.

Many functions have been modified to reduce the number of times
structures are passed as arguments, rather than pointers.

>>February 23, 2007

The threading strategy has been modified slightly to separate the end
of the search phase (and a complete reading of all results buffers)
from the termination phase.  This will allow future threading of
subsequent phases, including the Smith-Waterman alignments in
showbest() and showalign() (though care will be required to ensure
that the results are presented in the correct order).

>>February 20, 2007	fasta-34_27_0  (released as fasta-35_1)

The FASTA programs have been restructured to reduce the differences
between the threaded and unthreaded versions (and ultimately the
parallel versions) and to make more efficient use of modern large
memory systems.  This is the beginning of a move towards a more robust
shuffling strategy when searching databases with modest numbers of
related sequences.

The major changes:

  comp_lib.c -> comp_lib2.c  - comp_lib.c will be removed
  work_thr.c -> work_thr2.c  - work_thr.c will be removed

  mshowbest.c, mshowalign.c have been modified to remove aa1 as an
    argument. They must allocate that space if they need it.

  The system is set up to allocate a substantial amount of library
  sequence memory, either to a single buffer (unthreaded) or to the
  threaded buffer pool.  For smaller databases, the library sequences
  are read once, and then subsequently read from memory (this could be
  extended for RANLIB(bline) as well).

Soon, these changes will allow the program to re-read the beststr[]
sequences and shuffle them to produce accurate lambda/K estimates.

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See readme.v34t0 for earlier changes.

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