+++ /dev/null
-
- $Name: fa_34_26_5 $ - $Id: readme.v33t0,v 1.45 2001/07/10 18:03:42 wrp Exp $
-
-================ readme.v33t0 ================
-
-This release includes an MPI implementation of the parallel
-library-vs-library comparison code. See readme.mpi_3.3 and
-readme.pvm_3.3 for more information.
-
-=====
->>July 9, 2001
-
-Considerable changes to support no-global library functions.
-
-(1) Separate ascii/sequence mapping arrays are used by the
- query-reading (qascii), library-reading (lascii), and sequence
- comparison function (pascii) routines. As a result, there is no
- longer a need for tgetlib.o/lgetlib.o - lgetlib.o can serve both
- functions.
-
-(2) This also allows us to remove all #ifdef TFAST/FASTX conditionals
- from complib.c/comp_thr.c/p2_complib.c. We no longer need
- tcomp_thr.o, comp_thrx.o, etc. We still have a variety of
- p2_complib.o variations to support the different c34.work* files.
-
-(3) Because non-global openlib/getlib functions are available, exactly
- the same open/get functions are available for reading both the
- query and reference libraries in pv34comp* programs. The
- host-specific openlib/getlib functions in hxgetaa.c are now
- provided by nmgetlib.c, etc. This has two effect:
-
- (a) it is now possible to compare a query database generated by an
- SQL query to a library database generated by a different SQL
- query.
-
- (b) pv34comp* has lost (at least in this version) the ability to
- automatically detect the query sequence type. To search with a
- DNA query, you MUST use "-n".
-
-(4) the resetp() function is now responsible for almost all of the
- function sepcific (TFAST/FASTX/etc) initializations. All of the
- function specific code has been removed from complib.c/comp_thr.c
- and most of it has been moved to initfa.c/resetp().
-
-(5) manageacc.c has been merged into compacc.c (mostly prhist()).
-
-(6) Although it may reflect a subtle bug in my code, it is not
- possible to reliably run threaded/memory mapped versions of the
- fasta34_t code. I have spent considerable time tracking down the
- problem, and have determined that, in threaded code, something
- happens during the thread initialization to corrupt the
- description offset information used when files are memory mapped.
- This never occurs when the unthreaded versions of the code are
- used. And it does not occur under MacOSX, Compaq Tru64Unix, Sun
- Solaris/Sparc, or SGI IRIX.
-
- Thus, I cannot recommend using the threaded code versions (_t)
- under Linux (RH6.2 or 7.1).
-
-=====
->>June 1, 2001
-
-Many changes to accomodate a new - no global variable - strategy for
-reading sequence databases. Every time a file is opened, a struct
-lmf_str is allocated which can be used for memory mapped files, ncbl2,
-files, and mysql files.
-
-In addition, an open'ed file has a default sequence type: DNA or
-protein, or one can open a file in a mode that will allow the sequence
-type to be changed.
-
-=====
->>May 18, 2001 CVS: fa33t09d0
-
-A new compile time parameter - -DGAP_OPEN, is available to change the
-definition of the "-f gap-open" parameter from the penalty for the
-first residue in a gap to a true gap-open penalty, as is used in BLAST
-and many other comparison algorithms. This will probably become the
-default for fasta in version 3.4.
-
-Fixes to conflicts between "-S" and "-s matrix". When a scoring
-matrix file was specified, lower-case alignments were not displayed
-with -S (although the scores were calculated properly).
-
-More extensive testting of mysql_lib.c (mySQL query-libraries) with
-the pv4comp* and mp4comp* programs.
-
-=====
->>April 5, 2001 CVS: fa33t08d4b3
-
-Changes in nmgetlib.c and ncbl2_mlib.c to return long sequence
-descriptions for PCOMPLIB (pv4/mp3comp*). Also fix p2_complib.c to
-request DNA library for translated comparisons.
-
-Fix for prss33(_t) to read both sequences from stdin.
-
-=====
->>March 27, 2001 CVS: fa33t08d4
- --> fa33t08d4
-
-Problems in ncbl2_mlib.c found searching NCBI non-redundant nucleotide
-database "nt" were fixed. Testing revealed a minor memory leak, which
-was fixed by modifying showbest.c, showalign.c, comp_thr.c, complib.c,
-and p2_complib.c to remember the last opened database file more
-effectively.
-
-Modifications to allow 64-bit fseek/ftell on machines like Sun,
-Linux/Intel, that support -D_FILE_OFFSET_BITS=64, -D_LARGE_FILE_SOURCE
-off_t, and fseeko(), ftello() with the option -DUSE_FSEEKO. Machines
-with 64-bit long's do not need this option. Machines with 32-bit
-longs that allow files >2 Gb can do so with 64-bit file access
-functions, including fseeko() and ftello(), which work with off_t file
-offsets instead of long's.
-
-=====
->>March 3, 2001 CVS: fa33t08d2
-
-Corrected problems in nmgetaa.c and mysql_lib.c with parallel
-programs, and one serious problem with alternate DNA scoring matrices
-(initfa.c, initsw.c) not being set properly. A subtle problem with
-the merge of scaleswn.c and scaleswg.c is fixed.
-
->>February 17, 2001
-
-Modified mysql_lib.c to use "#", rather than "%ld", to indicate the
-position of the GID. This change was made because sprintf() cannot be
-used reliably to generate an SQL string, as '"' and '%' are used in
-such strings.
-
-=====
->>January 17, 2001
-(no version change, date change)
-
-Minro fixes to initfa.c, initsw.c to deal with DNA scoring matrices
-properly. "-n -s dna.mat" is required for the sequence/matrix to be
-recognized as DNA.
-
->>January 16, 2001
--->v34t00
-
-Merge of the main CVS trunk - fa33t06 with the latest release branch,
-fa33t08.
-
-In addition, PCOMPLIB mods have been made to mysql_lib.c. Because
-p2_complib.c gets sequence description information during the first
-read of the database, the mysql_query must be changed to return:
-result[0]=GID, result[1]=description, result[2]=sequence. In the
-PCOMPLIB case, the other SQL queries (for GID description, sequence)
-are not necessary but must still be provided.
-
-=====
->>January 16, 2001
-(no version change, previous version not released)
-
-changes to p2_complib.c to correct openlib() incompatibility.
-
-changes to nmgetaa.c, ncbl2_lib.c to incorporate PCOMPLIB. nxgetaa.c
-removed.
-
-=====
->>January 12, 2001
-(no version change, previous version not released)
-
-Change to initfa.c to move ktup check from query_parm() to last_init().
-
-=====
->>January 10, 2001
---> v33t08
-
-Fixes to complib.c, comp_thr.c to deal properly with long query
-protein sequences when a short library chunk (e.g. -N 5000) was given.
-In the case where the chunk size is too short, it will be reset to a
-length which allows the search to proceed, by including an amount of
-new sequence that is equal to the amount of overlap sequence.
-
-scaleswn.c and scaleswg.c have been merged.
-
-v33t08 includes the initial implementation for mySQL described below
-for v33t07x.
-
-======
->>Dec. 20, 2000
---> v33t07x
-
-Initial implementation of a syntax for mySQL database queries. A new
-file, mysql_lib.c has been added, and changes have been made to
-nmgetaa.c (which should now replace nxgetaa.c) and altlib.h. A mySQL
-database search needs a file with 4 parts:
-
-(1) description of the database, user, password
-(2) a select statement that generates the set of protein sequences
- as: UID, sequence
-(3) a select statement that generates a UID, description given a UID
-(4) a select statement that generats a single UID, sequence given a UID
-
-Each of the four parts should be separated by ';'. For example, in
-the database that we are using for testing, a file "demo.sql" that
-contains:
-
-================
-localhost taxonomy username secret;
-SELECT proteins.gid, proteins.sequence FROM proteins,swissprot WHERE proteins.gid=swissprot.gid AND swissprot.spid IS NOT NULL;
-select proteins.gid, concat(swissprot.spid," ",proteins.description) from proteins,swissprot where proteins.gid=%ld AND swissprot.gid=proteins.gid;
-select gid, sequence from proteins where gid=%ld;
-================
-
-will find all the proteins in the BLAST "nr" database that also have
-SwissProt ID's when given the command line:
-
- fasta33 -q query.aa "demo.sql 16"
-
-At least for simple queries, there is surprisingly little overhead for the
-search. For more complex queries involving several tables, the overhead
-can be significant.
-
-At the moment, libraries that need the functions in mysql_lib.c will
-use library type 16. We may also use file type 17 for SQL queries
-that return binary sequences.
-
-This implementation of mysql_lib.c was written to require a minimal
-amount of change to the other programs. Only nmgetaa.c and altlib.h
-needed to be changed to incorporate this new capability. One result
-of this limitation is that one cannot mix mySQL databases queries with
-other databases in the same search. Eventually, I would like to make
-a mySQL database like any other, so that several mysql database
-queries could be searched in the same run, and mysql databases could
-be mixed with other (flat file) databases, but this will require some
-changes in the function calls throughout the code. (Right now, the
-various programs do not distinguish between an openlib() that is made
-before searching a large database, and one before retrieving a single
-sequence. This must be changed for a database query like mySQL to
-behave like other databases.
-
-Several mySQL demo files have been provided: mysql_demo*.sql.
-
-(10 January 2001) The mySQL code has been tested on Intel Linux and
-Compaq/Alpha/Tru64 Unix.
-
->>Dec. 9, 2000
-
-Changes to apam.c that to tie different default gap penalties to
-alternate scoring matrices. In addition, changes to apam.c, to deal
-with user-specified matrices with or without '*'.
-
->>Nov. 5, 2000 (date updated)
-
-pst.dnaseq can now have 3 values, -1, or 0-> protein, 1->DNA, and 2->other.
-This becomes important for thing like init_karlin_a, which needs a
-background frequency of residues.
-
->>Nov. 1, 2000
-
-Significant bug fixes for the -z 6/-z 16 option. An ininitialized
-variable was fixed in karlin.c, and comp_thr.c did not pass the
-correct composition argument type in find_zp(). The -z 6/16 option
-has now been tested and works correctly on Alphas, Linux x86, SGI, Sun
-and Mac OSX. Another problem was fixed in scaleswn.c (simplex()) that
-prevented the code from being reused by the pv4/mp4 complib programs.
-
->>Oct. 9, 2000
-
-Several changes made to accomodate Mac OSX. Longer lists of superfamily
-numbers now supported in p[su]4comp/m[su]4comp programs.
-
->>Sept 25, 2000
-
-All global variables have been removed from scaleswn.c. The last to
-go, db_struct db, required many edits, because until now, the fasta
-programs have kept two versions of the db_struct data (entries,
-length). One version was kept by the main program, which updated entry
-number and db length as sequences were read; a second copy of this
-information was kept by the statistical estimation routines. Now
-there is only one copy, which means that the E() values will be a
-function of the complete database, not the database with some high
-scoring sequences removed.
-
->>Sept 23, 2000
-
-Continued removal of global variables from scaleswn.c. Only one
-global is left, db_struct db, which contains the number of entries in
-the database and the number of residues. It will be the next to go
-(changing all the zs_to_*() functions) and scaleswn. will be free
-of globals. scaleswg.c is gone - scaleswn.c compiles to scaleswg.c
-with -DNORMAL_DIST.
-
->>Sept 20, 2000
-
-Removal of histogram globals required changes in p2_complib.c as well.
-p_complib.c has not been updated. scaleswg.c has been modified to
-reflect the new histogram strategy.
-
->>Sept 19, 2000
-
-Substantial changes to remove globals for printing histogram. m_msg
-now contains a hist_str, which keeps histogram information.
-
->>Sept. 19, 2000
-(no version change, previous version not released)
-
-Correct bug introduced into scaleswn.c (inithist()) by changing
-score2_sums[], score_sums[] from int to double.
-
-Reporting of version numbers is more consistent between fasta33,
-fasta33_t, and pv4compfa/mp4compfa. The programs now report the same
-numbers/dates in similar places.
-
->>Sept. 15, 2000
---> v33t07
-
-Changes to fix problems with statistical estimates when a large
-fraction (but not all) of the database is related. Several users
-reported problems when searching with rRNA genes with version 33t06.
-In some cases, a 100% identitical match over 1500 nt would not be
-statistically significant against a search of the bacterial division
-of Genbank. This problem was not seen with some releases of v33t05.
-
-The cause of the problem was a change between v33t05 and v33t06 to
-allow scoring matrices with unusual scaling to be used. In v33t05,
-there was a line that excluded all scores > 300 from the statistical
-estimation procedure. While 300 is a high score with any "normal"
-scoring matrix, some investigators were using matrices scaled 10X, so
-that a score of 300 was really a score of 30 with a conventional
-matrix, and should not be excluded. Unfortunately, removing the test
-to exclude scores > 300 meant that when a rRNA sequence was used to
-search the bacterial division, tens of thousands of high scoring
-related sequences were treated as if they were unrelated, with the
-result that the variance estimates were much too high, and thus high
-real scores had low z-scores, and thus were not statistically
-significant. (There appear to be more than 20,000 rRNA sequences in
-the bacterial division of Genbank, almost 25% of all sequences).
-
-The solution to the problem is a substantial enhancement in the
-strategies used to exclude high-scoring, related sequences, the -z 1,
-4, and 5 parameter estimation strategies. The programs now estimate
-the expected high scoring sequence by calculating an ungapped Lambda
-and K, and then use a relatively conservative threshold for excluding
-scores that are higher than would be expected 0.01 times by chance.
-By calculating Lambda and K, we can scale the cutoff thresholds to
-allow scoring matrices with unusual scales. For "normal" searches,
-there should be little change, but there should be an improvement for
-searches with large numbers of related sequences in the database.
-
-As a result of testing for this change, a bug in the karlin() function
-used with -z 6 was found and corrected.
-
-=======
->>Sept. 9, 2000
-
-Changes to manshowbest.c to include correct display coordinates.
-
-Significant changes to structs.h, param.h, p2_complib.c,
-p2_workcomp.c, to store and use a reliable a_struct for alignment
-coordinates.
-
-Other cosmetic changes.
-
->>Sept. 7, 2000
-
-Minor changes to complib.c, showrss.c, so that prss33 -q uses 200
-shuffles and prss33 provides bit scores, rather than z-scores.
-(no version number change).
-
-Modifications to p2_complib.c to include superfamily numbers for
-ps4comp* ms4comp*.
-
->>Aug 22, 2000
-
-Changes to mmgetaa.c, ncbl2_mlib.c, dropfs.c to accomodate AIX.
-00README.1st updated to reflect the current version and correct
-outdated information on threads.
-
->>Aug. 3, 2000
-
-Modifications to initpam2() in initsw.c to correct a problem with pam_x
-when the -S option is used.
-
-Modifications to compacc.c, scaleswn.c to ensure that residue numbers
-are calculated properly when more than 2 Gb of sequence is searched.
-
->>July 12, 2000
-
-Modifications to dropnfa.c so that DNA matches to 'N' will be included
-in the "ungapped %identity". Thus, a sequence that is 100% identical
-for 100 nt on either side of a 100 nt region that has been masked to
-'NNNNN' will be reported as: "67% identical (100% ungapped)". This
-has been added to deal with masked BAC-end databases. It would be
-better if masking changed the letters to lowercase, but the mouse
-BAC-end sequences at TIGR use 'NNNNN'. This is currently available
-only for the fasta function, not [t]fast[x/y], etc, and only for DNA
-sequences.
-
-mk_n_pam() in apam.c modified to ensure that mismatch scores of -1
-remain -1.
-
->>June 25, 2000
-
-Modification to nxgetaa.c, nmgetaa.c, mmgetaa.c to return Genbank Accession
-number as part of the descriptive string.
-
->>June 11, 2000
-
-(no version change - not yet released)
-
-Modifications to calcons(), calc_id(), showbest(), p_workcomp.c to
-provide ngap_q (number of alignment gaps in query) , ngap_l (number
-of gaps in library) information for -m 9 output.
-
->>June 6, 2000
-
-(no version change - not yet released)
-
-Modified scaleswn.c to provide better support for unconventional
-scoring scoring matrices, in particular, scoring matrices where every
-value is 50-times higher. Previous versions of the MLE estimator (-z
-2) started with lambda = 0.2, which is too high for a scoring matrix
-going from -500:+1500. The initial estimate for lambda is now
-calculated using the formula: lambda = pi/sqrt(6*variance). For the
-default -z 1, a restriction to limit scores to a maximum of 300 for
-the statistical analysis was removed.
-
->>June 3, 2000
-
-Modified aligment output, and -m 9 and -m10, to report an "ungapped"
-identity as well as the traditional "gapped" identity. The
-traditional "gapped" identity reports the number of identities divided
-by the overall length of the alignment, including gaps. The
-"ungapped" identity does not include gaps in the length of the
-alignment. This new value is included for alignments that include
-introns; thus, a tfastx33 search might find the 100% identical genomic
-sequence but report the gapped percent identity if a short intron were
-included in the alignment (the alignment probably would not span a
-long exon) as 66%. The "ungapped" identity would remain 100%. The
-ungapped identity value is also shown in the "-m 9" output line after
-the "gapped" fraction identical.
-
->>June 1, 2000
-
-Modified -m 9 output to provide fraction identical, alignment boundary
-information with the initial list of high scoring sequences, just as
-the pv3comp and mp_comp versions do. The -m 9 option now shows the
-same alignment display as -m 0, but the width of the alignment is
-increased by 40. Thus, by default, -m 9 will show the list of best
-hits, with percent identity, Smith-Waterman score, and alignment
-boundaries initially, and then show alignments standard (-m 0)
-alignments with 100 residues/line.
-
->>May 29, 2000
-
-Correct some problems with reading data files with <CR>'s under unix.
-
-nmgetaa.c/nxgetaa.c/mmgetaa.c have been modified to convert <TAB>
-('\t') to <SPC> (' ') in descriptive lines.
-
-=======
-
->>May 3, 2000
-
- Corrected problem with very low mean_var in fit_llen() in scaleswn.c.
-
->>May 2, 2000
- (no version number change - previous version not released)
-
- Merged fasta33t05d2 with fasta33t06. Also removed restriction on
-"-M size-range" to proteins - the size range now can be applied to DNA
-as well.
-
->>May 1, 2000
- (changes to v33t05d merged into v33t06)
-
-Introduced changes to include '*' as a valid sequence character, which
-indicates termination. Thus, 'TGA', 'TAG', and 'TAA' are now
-tranlated to '*' rather than 'X', and the protein PAM matrices have
-been modified to provide a match score of approximately 1/2 the max
-identity score for a '*:*' match. Otherise, '*' is the same as 'X'.
-This change only affects query sequences that include a '*' to
-indicate an end of sequence, the '*' is not there by default.
-
-The inclusion of '*' broke some things in tfasts33, tfastf33, fasty33,
-and tfasty33, which were fixed today.
-
->>March 28, 2000/April 24, 2000
- --> v33t06
-
-(a) -z 6 statistics that factor in composition
-(b) -smatrix-offset pam-offset parameter
-
-(a) This release provides a new statistics option, -z 6, which
-provides a more sophisticated model that accounts for sequence
-composition. When -z 6 is used (only for fasta33(_t) and
-ssearch33(_t)), the program calculates a composition parameter
-comp=1/lambda using a modified version of the Karlin-Altschul karlin()
-function. As a result, every sequence in the database has an
-associated length (n1) and composition (comp).
-
-The length n1 and composition comp are used in the maximum likelihood
-estimation described by Mott (1992) Bull. Math. Biol. 54:59-75. Four
-parameters are estimated, a0, a1, a2, and b1, and the probability of
-obtaining a score is then:
-
-p(s >= x) = 1-exp(-exp(-( a0 + a1*comp + a2*comp*log(n0*n1) + x)/(b1*comp)))
-
-The maximum likelihood estimates of a0, a1, a2, and b1 are calculated
-using the Nelder-Mead simplex search strategy.
-
-The average Lambda is reported for the search using Lambda =
-1/(b1*ave_comp). Where ave_comp is the geometric mean of the comp values
-calculated during the statistical estimates.
-
-The "lambda/comp" calculation can fail for sequences with very biased
-amino acid composition. When this occurs, 'comp' is set to -1.0 (as
-is 'H', the information content parameter) and the 'ave_comp' value is
-used to calculate statistical significance. (But obviously 'ave_comp'
-is not really appropriate, since if the sequence had an average 'comp'
-value, it would have been calculated.) When -z 6 is used, the
-alignment display shows the 'comp' and 'H' values for that library
-sequence.
-
-(b) Scoring matrix offsets - The main reason that the "lamdba/comp"
-calculation fails is that, for the particular query/library sequence
-pair, the expected score is not < 0, instead, Sum {p_ij S_ij} >= 0.0.
-This problem is reported to 'stderr' when it occurs. The simplest
-solution to the problem is to provide an offset to the scoring matrix;
-for example, to use Blosum62 - 1, which ranges from +10 to -5, rather
-than the standard +11 to -4. This option used to be available with
-the -S offset option, but -S is now used to specify a lower-case
-seg-ed database. The offset can now be specified as part of the
-scoring matrix name. Thus, "-s BL62-1" uses Blosum62 reduced by 1 at
-each entry. The '-' character is used to indicate an offset, so
-scoring matrix files must not have a '-' in their name.
-Alternatively, "-s BL80+1" or "-s BL80--1" would add one to each value.
-
-nxgetaa.c, nmgetaa.c, and mmgetaa.c have been edited to avoid string
-run-off problems after strncpy().
-
-Fixed problem where positive gap extension penalties in ssearch33
-were not converted to negative values.
-
->>April 8, 2000
-
-Fixed problem in calculating corrected sequence lengths for
-Altschul-Gish probabilities.
-
->>March 30, 2000
- (no version change, date updated to March 30, 2000)
-
-Corrected problem with -m 9 option.
-
-The '*' character is now available to allow translated alignments to
-extend through the termination codon. Thus, if a protein sequence ends
-with a '*', and matches in to a translated termination codon, the
-score will be increased. The *:* match score is set to 1/2 the max
-positive score for the matrix (see upam.h). This strategy can also be
-used to upweight a match that extends all the way to the end of a
-full-length sequence by putting '*' at the end of both the query and
-library protein sequences. Recognition of '*' will probably become a
-command line option.
-
->>March 21, 2000
- (no version change, previous version not distributed)
-
-Changes to map_db.c, list_db.c, and mmgetaa.c to accomodate large
-sequence files. Long (64-bit on some systems) variables are now used
-to specify file and memory position for the memory mapped functions.
-As a result, there are now two *.xin (memory mapped index) file
-formats: MP0, which uses 32-bit longs, and MP1, which uses 64-bit
-longs. On 64-bit machines, MP0 32-bit indices are read properly, but
-limit the database size to 2 or 4 Gb; MP1 64-bit indices allow very
-large databases. Blast2.0 formatdb databases are still limited to
-4Gb. To compile map_db.c to generate 64-bit index files, include the
-compile time option -DBIG_LIB64 in the Makefile. (Currently this
-option has been tested only on the DEC Alpha and SGI platforms, and
-will work only with Unix versions that provide 64-bit longs and 64-bit
-ftell()'s.)
-
-The -R results file now uses sfn_cmp() to report a matching
-superfamily number, if one exists, and '0' otherwise.
-
->>March 12, 2000
- (no version change, previous version not distributed)
-
-Provide new strategy for specifying library abbreviations. In
-addition to:
-
- fasta33 query.aa %anr
-
-one can also specify:
-
- fasta33 query.aa %pir1+sp+nr
-or
- fasta33 query.aa +pir1+sp+nr
-or
- fasta33 query.aa %+pir1+sp+nr
-
-where the + anywhere in the library name string indicates that
-variable length library names, separated by '+', are being used (the
-last '+' is optional). The FASTLIBS file then becomes:
-
-================
-PIR1 Annotated Protein Database (rel 56)$0+pir1+/slib2/blast/pir1.lseg
-NBRF Protein database (complete)$0+nbrf+@/seqlib/lib/NBRF.nam
-NRL_3d structure database$0D/seqlib/lib/nrl_3d.seq 5
-NCBI/Blast non-redundant proteins$0+nr+/slib2/blast/nr.lseg
-NCBI/Blast Swissprot$0+sp+/slib2/blast/swissprot.lseg
-================
-
-The two abbreviation types, single letter and +word+, cannot be
-intermixed, and at least initially, +word+ specifiers are
-case-sensitive (single letter abbreviations are not) and will not be
-available interactively, only on the command line.
-
-Removed 'K' estimate for Expectation_n, Expectation_i fits to the
-distribution of unrelated similarity scores. 'K' cannot be calculated
-from the data available. 'Lamdba' can be calculated, it is
-1.28255/sqrt(mean_var), and is still available.
-
->>March 3, 2000
- (no version change)
-
-changed Makefile33.common, Makefile.common, to incorporate $(NRAND)
-rather than "rand48". Provide nrandom.c which uses random(), as
-replacement for nrand.c, which uses rand48().
-
->>February 8, 2000
- --> v33t05
-
-Fixes to scaleswn.c (proc_hist_ml) to set num_db_entries properly.
-Scaleswn.c also provides Lambda estimates for -z 1/11 (Expectation_n),
-and -z 1/14 (Expectation_i) statistical estimates.
-
-Modifications to calc_id() to correct bug in counting identities.
-Modified showalign() to use calc_id() with -m 9, for simpler
-debugging.
-
-Additional modifications to dropfa*.c files to deal properly with 'n's
-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
-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