readme.v33t0

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

and 'x's.

Added new option: -x #, which allows one to override the penalty for a
match against 'x' (or 'N') provided by the scoring matrix.  This
option is particularly useful in fast[x/y] searches, where out of
frame low complexity regions can generate high scores.

The old function of '-x' - to specify an alternate coordinate system,
is now available as '-X # #'.

Updated scaleswn.c to provide window shuffle information for -z 12.

Updated compacc.c, workacc.c, to fix serious bug in wshuffle()
that destroyed aa1[n1]=0.

>>January 25, 2000
  --> v33t04

  A serious bug in all of the fasta related programs has been
corrected.  The new code in fasta33 which ignores certain residues
failed to initialize one of the arrays properly.  As a result, in
pathological situations, a very strong match could be missed.

  Corrected minor bug in initsw.c that cause misplaced "ktup" command
line argument, which should be ingnored by ssearch, to be read as -d
ktup.

  Improved error message for 0 length query sequence.

>>January 17, 2000
  --> no external version number change

Modified mmgetaa.c, map_db.c, and nmgetaa.c to provide memory mapping
of genbank flatfile (format=1) files.  This format could be read much
more efficiently, however.

>>January 12, 2000
  --> no external version number change

Changed the behavior of the options that set the number of high scores
(-b) and alignments (-d) that are displayed.  Previously, fasta33 -E
10.0 -d 10 would show 50 best scores, rather than all the scores with
E() < 10.0.  To get the -E threshold to limit, -E 10.0 -b 10000 -d 10
was required. This is now fixed. Setting "-d 10" does not affect the
number of best scores shown.

Minor change in mw.h to remove unused defines.

fasta3x.me (fasta3x.doc) updated.

>>January 6, 2000
  --> v33t03

Corrected bug in memory mapped reads of gcg_binary format files
that potentially caused the last 63 residues to be read improperly.

Changes to comp_thr.c, pthr_subs.c, uthr_subs.c, ibm_pthr_subs.c to
ensure that each thread has its own work_info structure. This solves
some minor race conditions that sometimes caused some parameters
not to be reported properly.

Changes to most of the drop*.c files to correct some minor problems
with sequence alphabets. Code in mmgetaa.c (memory mapped code for
FASTA, GCG compressed files) reordered to prevent files from being
memory mapped if appropriate index files are not available.

See readme.pvm_3.3 for updates to the pvm programs.

>>December 10, 1999
  (no version change - modifications largely affect ps3comp*)

Modifications to showsum.c to deal with 2 scores/sequence.  Modifications
to mmgetaa.c for superfamily numbers.

>>December 7, 1999
 (no version change, previous version not released)

Corrected problem in mmgetaa.c that caused searches on a memory mapped
single long sequence (e.g. Chr22) to fail.  Corrected bug in map_db.c
that caused it to crash on some architectures if a filename was not
specified.  Corrected off-by-three error in fasty/tfasty.  Corrected
indexing error in dropfz2.c.

>>December 5, 1999
 --> v33t02 
 
corrected some bugs in inifa.c/initsw.c/doinit.c that caused
abbreviated function names to be lost.

modify showbest.c, showalign.c to include information on position in
library sequence (bbp->cont) to distinguish subsegment of very long
sequences.  Currently, the new label is available only with -m 6.

>>November 29, 1999
 [t]fastz33 uses v33t02 of fasty function.

Replace dropfz.c with dropfz2.c.  Dropfz2.c interprets any codons,
that include the nucleotide 'N' as the amino 'X'. Previously, 'N' was
treated as 'A', so 'NNN' ended up 'K'.  This modification, together
with the -S option and lower-case pseg'ed databases, should ensure
that DNA queries with large numbers of 'N's do not match low
complexity regions.

>>November 20, 1999
 (no version change, previous version not released)

Modify initfa.c to disply initn, init1 scores for [t]fast[fs].
Include "-B" option to show previous z-scores.

>>November 17, 1999
 (no version change, previous version not released)
 
Modify dropfx.c to use saatran(), rather than aatran().  saatran
translates any 'N' containing codon as 'X'.  aatran() treats 'N' as
an 'A'.  Although more steps are required for translation, the program
appears to run just as fast.

>>November 7, 1999
 --> v33t01

Substantial changes to the output format in showbest.c (the list of
high scoring sequences) and showalign.c (the alignments).  The classic
list of best scores:

The best scores are:                             initn init1 opt z-sc E(82014)
gi|121716|sp|P10649|GTM1_MOUSE GLUTATHIO  ( 218) 1497 1497 1497 1761.1 2.3e-91
gi|121717|sp|P04905|GTM1_RAT GLUTATHIONE  ( 218) 1413 1413 1413 1662.9 6.7e-86

has been replaced by:

The best scores are:                                       opt bits E(82138)
gi|121716|sp|P10649|GTM1_MOUSE GLUTATHIONE S-TRAN  ( 218) 1497 354 7.6e-98
gi|121717|sp|P04905|GTM1_RAT GLUTATHIONE S-TRANSF  ( 218) 1413 335 5.3e-92

This display provides more information and removes the outdated initn
and init1 scores, which are no longer used. The "bit" score is
comparable to the blast2 bit score.  It is calculated as: (lambda*S -
ln K)/ln 2, where S is the raw similarity score, lambda and K are
statistical parameters estimated from the distribution of unrelated
sequence similarity scores.  All of the similarity scores, including
init1, initn, and z-scores are reported with the alignment data.
Z-scores are displayed instead of bit scores in the list of high
scores if the command line option "-B" is specified.

In addition, the alignment score line has changed from:

>>gi|2506495|sp|P20136|GTM2_CHICK GLUTATHIONE S-TRANSFER  (220 aa)
 initn: 954 init1: 954 opt: 958 Z-score: 1130.9 expect() 1.1e-56
Smith-Waterman score: 958;  61.927% identity in 218 aa overlap (1-218:1-218)

to:

>>gi|2506495|sp|P20136|GTM2_CHICK GLUTATHIONE S-TRANSFER  (220 aa)
 initn: 954 init1: 954 opt: 958  Z-score: 1130.9  bits: 216.4 E(): 2.8e-56
Smith-Waterman score: 958;  61.927% identity in 218 aa overlap (1-218:1-218)

In addition to the addition of the "bits:" score, the "expect()" label
has changed to "E()" to save some space.

>>November 4,12, 1999
(no version change)

Fixed serious bug in -z 2 lambda/K calculation in scaleswn.c

Fixed bugs in llgetaa.c (openlib()) and definition of superfamily
numbers.

>>October 21, 1999
(no version change)

Begin using CVS for version control. Correct faulty error message in
dropfs.c.  Corrected bad "goto loopl;" in dropfz.c.  Corrected prss3.rsp
for Makefile.tc (Win32 version).

>>October 18, 1999
 --> v33t0

Corrected some serious bugs with the various fasta/x/y programs when
the -DALLOCN0 was used to save memory.  Improvements to fasta3x.me/.doc
documentation.

>>October 12, 1999
 --> v33tx

For this initial release of version 33 of the FASTA programs, the
Makefile's have been modified to make "fasta33(_t)", "fastx33(_t)",
etc, so that you can test fasta33 while retaining fasta3 (from release
v32t08).  The FASTA33 programs are somewhat slower than previous
releases, but I believe the ability to handle low complexity regions
without 'X'ing them out outweighs the slowdown.  By (temporarily)
changing the names of the programs slightly, it will be easier for you
to judge the relative cost and benefit.  To "make" the programs as
"fasta3(_t)", etc, simply replace "Makefile33.common" with
"Makefile.common" in the "Makefile" that you use.

>>September 30, 1999

ssearch3/fasta3/fastx3/fasty3 have been modified to search databases
containing both upper and lower case letters, where lower case letters
indicate low-complexity regions.  With the modified programs, lower
case letters are treated as 'X's' in the initial scan, but are then
treated normally in the final alignment.  In addition, alignments can
contain lower case letters.  Lower case letters are treated as
low-complexity regions during the seach phase of the program, but as
"conventional" residues during the alignment phase, with the "-S"
option.  Currently, lower case letters are mapped to 'X's during the
scan of the entire library.  In the future, alternate weights will be
available. This is a substantial improvement for very large scale
comparison, where one seeks both accurate statistical estimates and
accurate %identities and alignments, and for translated DNA:protein
comparisons, like "fastx3" and "fasty3", where out-of-frame
translations tend to match low complexity regions (see Pearson et
al. (1997) Genomics 46:24-36).

Protein databases (and query sequences) can be generated in the
appropriate format using John Wooton's "pseg" program, available from
ftp://ncbi.nlm.nih.gov/pub/seg/pseg.  Once you have compiled the "pseg"
program, use the command:

	pseg database.fasta -z 1 -q  > database.lc_seg

Once you have database.lc_seg, run the command "map_db" to generate
a ".xin" file that can be used to efficiently memory map the database.

You can then search database.lc_seg with or without the "-S" option.
Without "-S", the database is treated as any other FASTA format file -
all the residues are present.  With "-S", lower case residues will be
treated as 'x's' during the initial scan but as normal residues when
final alignments are displayed.

When the -S option is used, the matrix information line is changed
from: "BL50 matrix (15:-5)" to "BL50 matrix (15:-5)xS".  The "-S"
option is no longer available to provide a scoring matrix offset.

Unfortunately, Blast2.0 format files cannot contain lower case
letters.  We have addressed this problem by providing efficient memory
mapped access to Fasta and GCG/PIR, and GCG/compressed-binary files in
the last release of fasta32t08. The memory mapped file I/O
improvements are provided in fasta33 as well.

================ readme.v32 ================

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 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