+++ /dev/null
-
-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
- --> v32t06
-
-Corrected bug in complib.c (fasta3, fastx3, etc) that caused core
-dumps with "-o" option.
-
-Corrected a subtle bug in fastx/y/tfastx/y alignment display.
-
->>June 30, 1999 - new distribution
-(no version change)
-
-Corrected doinit.c to allow DNA substitution matrices with -s matrix
-option.
-
-Changed ".gbl" files to ".h" files.
-
->>June 2 - 9, 1999 - new distribution
-(no version change)
-
-Added additional DNA lambda/K/H to alt_param.h. Corrected some
-other problems with those table. for the case where (inf,inf)
-gap penalties were not included.
-
-Fixed complib.c/comp_thr.c error message to properly report filename
-when library file is not found.
-
-Included approximate Lambda/K/H for BL80 in alt_parms.h.
-BL80 scoring matrix changed from 1/3 bit to 1/2 bit units.
-
-Included some additional perl files for searchfa.cgi, searchnn.cgi
-in the distribution (my-cgi.pl, cgi-lib.pl).
-
->>May 30, 1999, June 2, 1999 - new distribution
-(no version number change)
-
-Added Makefile.NetBSD, if !defined(__NetBSD__) for values.h. Changed
-zs_to_E() and z_to_E() in scaleswn.c to correctly calculate E() value
-when only one sequence is compared and -z 3 is used.
-
->>May 27, 1999
-(no version number change)
-
-Corrected bug in alignment numbering on the % identity line
- 27.4% identity in 234 aa (101-234:110-243)
-for reverse complements with offset coordinates (test.aa:101-250)
-
->>May 23, 1999
-(no version number change)
-
-Correction to Makefile.linux (tgetaa.o : failed to -DTFAST).
-
->>May 19, 1999
-(no version number change)
-
-Minor changes to pvm_showalign.c to allow #define FIRSTNODE 1.
-Changes to showsum.c to change off-end reporting. (Neither of these
-changes is likely to affect anyone outside my research group.)
-
->>May 12, 1999
- --> v32t05
-
-Fixed a serious bug in the fastx3/tfastx3 alignment display which
-caused t/fastx3 to produce incorrect alignments (and incorrectly low
-percent identities). The scores were correct, but the alignment
-percent identities were too low and the alignments were wrong.
-
-Numbering errors were also corrected in fastx3/tfastx3 and
-fasty3/tfasty3 and when partial query sequences were used.
-
->>May 7, 1999
-
-Fixed a subtle bug in dropgsw.c that caused do_work() to calculate
-incorrect Smith-Waterman scores after do_walign() had been called.
-This affected only pvcompsw searches with the "-m 9" option.
-
->>May 5, 1999
-
-Modified showalign.c to provide improved alignment information that
-includes explicitly the boundaries of the alignment. Default
-alignments now say:
-
-Smith-Waterman score: 175; 24.645% identity in 211 aa overlap (5:207-7:207)
-
->>May 3, 1999
-
-Modified nxgetaa.c, showsum.c, showbest.c, manshowun.c to allow a
-"not" superfamily annotation for the query sequence only. The
-goal is to be able to specify that certain superfamily numbers be
-ignored in some of the search summaries. Thus, a description line
-of the form:
-
->GT8.7 | 40001 ! 90043 | transl. of pa875.con, 19 to 675
-
-says that GT8.7 belongs to superfamily 40001, but any library
-sequences with superfamily number 90043 should be ignored in any
-listing or summary of best scores.
-
-In addition, it is now possible to make a fasta3r/prcompfa, which is
-the converse of fasta3u/pucompfa. fasta3u reports the highest scoring
-unrelated sequences in a search using the superfamily annotation.
-fasta3r shows only the scores of related sequences. This might be
-used in combination with the -F e_val option to show the scores
-obtained by the most distantly related members of a family.
-
->>April 25, 1999
-
- -->v32t04 (not distributed)
-
-Modified nxgetaa.c to remove the dependence of tgetaa.o on TFASTA
-(necessary for a more rational Makefile structure). No code changes.
-
->>April 19, 1999
-
-Fixed a bug in showalign.c that displayed incorrect alignment coordinates.
-(no version number change).
-
->>April 17, 1999
-
- --> v32t03
-
-A serious bug in DNA alignments when the sequence has been broken into
-multiple segments that was introduced in version fasta32 has been
-fixed. In addition, several minor problems with -z 3 statistics on
-DNA sequences were fixed.
-
-Added -m 9 option, which unfortunately does different things in
-pvcompfa/sw and fasta3/ssearch3. In both programs, -m 9 provides the
-id's of the two sequences, length, E(), %_ident, and start and end of
-the alignment in both sequences. pvcompfa/sw provides this
-information with the list of high scoring sequences. fasta3/ssearch3
-provides the information in lieu of an alignment.
-
->>March 18, 1999
-
- --> v32t02
-
-Added information on the algorithm/parameter description line to
-report the range of the pam matrices. Useful for matrices like
-MD_10, _20, and _40 which require much higher gap penalties.
-
->>March 13, 1999 (not distributed)
-
- --> v32t01
-
- -r results.file has been changed to -R results.file to accomodate
- DNA match/mismatch penalties of the form: -r "+1/-3".
-
->>February 10, 1999
-
-Modify functions in scalesw*.c to prevent underflow after exp() on
-Alpha Linux machines. The Alpha/LINUX gcc compiler is buggy and
-doesn't behave properly with "denormalized" numbers, so "gcc -g -m
-ieee" is recommended.
-
-Add "Display alignments also (y/n)[n] "
-
-pvcomplib.c again provides alignments!! In addition, there is a
-new "-m 9" option, which reports alignments as:
-
->>>/home/wrp/slib/hlibs/hum0.aa#5>HS5 gi:1280326 T-cell receptor beta chain 30 aa, 30 aa vs /home/wrp/slib/hlibs/hum0.seg library
-HS5 30 HS5 30 1.873e-11 1.000 30 1 30 1 30
-HS5 30 HS2249 40 1.061e-07 0.774 31 1 30 7 37
-HS5 30 HS2221 38 1.207e-07 0.833 30 1 30 7 35
-HS5 30 HS2283 40 1.455e-07 0.774 31 1 30 7 37
-HS5 30 HS2239 38 1.939e-07 0.800 30 1 30 7 35
-
-where the columns are:
-
-query-name q-len lib-name lib-len E() %id align-len q-start q-end l-start l-end
-
->>February 9, 1999
-
-Corrected bug in showalign.c that offset reverse complement alignments
-by one.
-
->>Febrary 2, 1999
-
-Changed the formatting slightly in showbest.c to have columns line up better.
-
->>January 11, 1999
-
-Corrected some bugs introduced into fastf3(_t) in the previous version.
-
->>December 28, 1998
-
-Corrected various problems in dropfz.c affecting alignment scores
-and coordinates.
-
-Introduced a new program, fasts3(_t), for searching with peptide
-sequences.
-
->>November 11, 1998
-
- --> v32t0
-
-Added code to correct problems with coordinate number in long library
-sequences with tfastx/tfasty. With this release, sequences should be
-numbered properly, and sequence numbers count down with reverse
-complement library sequences.
-
-In addition, with this release, fastx/y and tfastx/y translated
-protein alignments are numbered as nucleotides (increasing by 3,
-labels every 30 nucleotides) rather than codons.
-
git://source.jalview.org / jabaws.git / blobdiff