readme.v32t0

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

FASTX/Y and FASTA (DNA) are now half as fast, because the programs now
search both the forward and reverse strands by default.

The documentation in fasta3x.me/fasta3x.doc has been substantially
revised.

>>October 9, 1999
 --> v32t08 (no version number change)

Added "-M low-high" option, where low and high are inclusion limits
for library sequences.  If a library sequence is shorter than "low" or
longer than "high", it will not be considered in the search.  Thus,
"-M 200-250" limits the database search to proteins between 200 and
250 residues in length.  This should be particularly useful for fasts3
and fastf3.  This limit applies only to protein sequences.

Modified scaleswn.c to fall back to maximum likelihood estimates of
lambda, K rather than mean/variance estimates. (This allows MLE
estimation to be used instead of proc_hist_n when a limited range of
scores is examined.)

>>October 20, 1999
(no version change)

Modify nxgetaa.c/nmgetaa.c to recognize 'N' as a possible DNA character.

>>October 9, 1999
 --> v32t08 (no version number change)

Added "-M low-high" option, where low and high are inclusion limits
for library sequences.  If a library sequence is shorter than "low" or
longer than "high", it will not be considered in the search.  Thus,
"-M 200-250" limits the database search to proteins between 200 and
250 residues in length.  This should be particularly useful for fasts3
and fastf3.  -M -500 searches library sequences < 500; -M 200 -
searches sequences > 200. This limit applies only to protein
sequences.

Modified scaleswn.c to fall back to maximum likelihood estimates of
lambda, K rather than mean/variance estimates. (This allows MLE
estimation to be used instead of proc_hist_n when a limited range of
scores is examined.)

>>October 2, 1999
 --> v32t08

Many changes:

(1) memory mapped (mmap()ed) database reading - other database reading fixes
(2) BLAST2 databases supported
(3) true maximum likelihood estimates for Lambda, K
(4) Misc. minor fixes

(1) (Sept. 26 - Oct. 2, 1999) Memory mapped database access.
It is now possible to use mmap()ed access to FASTA format databases,
if the "map_db" program has been used to produce an ".xin" file.  If
USE_MMAP is defined at compile time and a ".xin" file is present, the
".xin" will be used to access sequences directly after the file is
mmap()ed.  On my 4-processor Alpha, this can reduce elapsed time by
50%. It is not quite as efficient as BLAST2 format, but it is close.

Currently, memory mapping is supported for type 0 (FASTA), 5
(PIR/GCG ascii), and 6 (GCG binary).  Memory mapping is used if a
".xin" file is present. ".xin" files are created by the new program
"map_db".  The syntax for "map_db" is:

	map_db [-n] "/dir/database.fa"

which creates the file /dir/database.fa.xin.  Library types can be
included in the filename; thus:

	map_db -n "/gcggenbank/gb_om.seq 6"

would be used for a type 6 GCG binary file. 

The ".xin" file must be updated each time the database file changes.
map_db writes the size of the database file into the ".xin" file, so
that if the database file changes, making the ".xin" offset
information invalid, the ".xin" file is not used. "list_db" is
provided to print out the offset information in the ".xin" file.

(Oct 2, 1999) The memory mapping routines have been changed to
allow several files to be memory mapped simultaneously. Indeed, once a
database has been memory mapped, it will not be unmap()ed until the
program finishes.  This fixes a problem under Digital Unix, and should
make re-access to mmap()ed files (as when displaying high scores and
alignments) much more efficient.  If no more memory is available for
mmap()ing, the file will be read using conventional fread/fgets.

(Oct 2, 1999) The names of the database reading functions has been
changed to allow both Blast1.4 and Blast2.0 databases to be read.  In
addition, Makefile.common now includes an option to link both
ncbl_lib.o and ncbl2_lib.o, which provides support for both libraries.
However, Blast1.4 support has not been tested.

The Makefile structure has been improved.  Each architecture specific
Makefile (Makefile.alpha, Makefile.linux, etc) now includes
Makefile.common.  Thus, changes to the program structure should be
correct for all platforms.  "map_db" and "list_db" are not made with
"make all".

The database reading functions in nxgetaa.c can now return a database
length of 0, which indicates that no residues were read.  Previously,
0-length sequences returned a length of 1, which were ignored.
Complib.c and comp_thr.c have changed to accommodate this
modification.  This change was made to ensure that each residue,
including the last, of each sequence is read.

Corrected bug in nxgetaa.c with FASTA format files with very long
(>512 char) definition lines.

(2) (September 20, 1999) BLAST2 format databases supported

This release supports NCBI Blast2.0 format databases, using either
conventional file reading or memory mapped files.  The Blast2.0 format
can be read very efficiently, so there is only a modest improvement in
performance with memory mapping.  The decision to use mmap()'ed files
is made at compile time, by defining USE_MMAP.  My thanks to Eamonn
O'Toole of DEC/Compaq, and Daryl Madura of Sun Microsystems, for
providing mmap()'ed modifications to fasta3.  On my machines, Blast2.0
format reduces search time by about 30%.  At the moment, ambiguous DNA
sequences are not decoded properly.

(3) (September 30, 1999) A new statistical estimation option is
available.  -z 2 has been changed from ln()-scaling, which never
should have been used, to scaling using Maximum Likelihood Estimates
(MLEs) of Lambda and K.  The MLE estimation routines were written by
Aaron Mackey, based on a discussion of MLE estimates of Lambda and K
written by Sean Eddy.  The MLE estimation examines the middle 95% of
scores, if there are fewer than 10000 sequences in the database;
otherwise it excludes (censors) the top 250 scores and the bottom 250
scores.  This approach seems to effectively prevent related sequences
from contaminating the estimation process.  As with -z 1, -z 12 causes
the program to generate a shuffled sequence score for each of the
library sequences; in this case, no censoring is done.  If the
estimation process is reliable, Lambda and K should not vary much with
different queries or query lengths.  Lambda appears not to vary much
with the comparison algorithm, although K does.

(4) Minor changes include fixes to some of the alignment display routines,
individual copies of the pstruct structure for each thread, and some
changes to ensure that every last residue in a library is available
for matching (sometime the last residue could be ignored).  This
version has undergone extensive testing with high-throughput sequences
to confirm that long sequences are read properly.  Problems with
fastf3/fasts3 alignment display have also been addressed.

>>August 26, 1999 (no version change - not released)

Corrected problem in "apam.c" that prevented scoring matrices from
being imported for [t]fasts3/[t]fastf3.

>>August 17, 1999
 --> v32t07

Corrected problem with opt_cut initialization that only appeared
with pvcomp* programs.

Improved calculation of FASTA optcut threshold for DNA sequence
comparison for match scores much less than +5 (e.g. +3).  The previous
optcut theshold was too high when the match penalty was < 4 and
ktup=6; it is now scaled more appropriately.

Optcut thresholds have also been raised slightly for
fastx/y3/tfastx/y3.  This should improve performance with minimal
effects on sensitivity.

>>July 29, 1999
(no version change - date change)

Corrected various uninitialized variables and buffer overruns
detected.

>>July 26, 1999 - new distribution
(no version change - v32t06, previous version not released)

Changed the location of "(reverse complement)" label in tfasta/x/y/s/f
programs.

Statistical calculations for tfasta/x/y in unthreaded version
corrected.  Statistical estimates for threaded and unthreaded versions
of the tfasta/x/y/s/f programs should be much more consistent.

Substantial modifications in alignment coordinate calculation/
presentation.  Minor error in fastx/y/tfastx/y end of alignment
corrected.  Major problems with tfasta alignment coordinates
corrected.  tfasta and tfastx/y coordinates should now be consistent.

Corrected problem with -N 5000 in tfasta/x/y3(_t) searches encountered
with long query sequences.

Updated pthr_subs.c/Makefile.linux to increase the pthreads stacksize
to try to avoid "cannot allocate diagonal arrays" error message.
Pthreads stacksize can be changed with RedHat 6.0, but not RedHat 5.2,
so Makefile.linux uses -DLINUX5 for RedHat5.* (no pthreads stack size).
I am still getting this message, so it has not been completely
successful.  Makefile.linux now uses -DALLOCN0 to avoid this problem,
at some cost in speed.

The pvcomp* programs have been updated to work properly with
forward/reverse DNA searches.  See readme.pvm_3.2.

>>July 7, 1999 - not released