+++ /dev/null
->>July 22, 1998
-
- --> v31t10
-
-Corrected problem with histogram when unscaled statistics used (e.g. prss3).
-
-Corrected problems with prss3 shuffled sequence prompt. Provided option
-to enter number of shuffles, window size, for prss3. Number of shuffles
-for prss3 can be entered as an option (-d #) or as the third argument
-on the command line (prss3 query lib 1000).
-
-Modified nrand.c, nrand48.c to use time to set random number.
-
-Corrected problems reading GCG formatted files with prss3.
-
-Corrected various problems with pvcomp* programs, but they still do
-not produce alignments with version 3.1.
-
-Two new programs, fastf3(_t) and tfastf3(_t) are available. These
-programs compare a set of mixed peptide sequences from an Edman
-sequencer to a protein (fastf3) or DNA (tfastf3) database, using
-the database sequences to de-convolve the peptide mixture.
-
-See fastf3.1
-
->>August 11, 1998
-
-(no version change)
-
-Modified initfa.c so that using '-n' on the fastx/fasty command line
-would not cause problems.
-
-Changed labeling of query sequence length for fastx/fasty from 'aa' to 'nt'.
-
->>August 18, 1998
-
-(no version change)
-
-Modified complib.c, comp_thr.c scaleswn.c, to report E()-value for only
-one related sequence if -z 3 is used.
-
->>August 23, 1998
-
- -->v31t11
-
-Some serious problems with prss3 have been corrected:
-
-(1) use dropnsw.c rather than dropgsw.c for more accurate low scores
-
-(2) modify estimation program; use scaleswe.c rather than scaleswn.c.
- scaleswe.c has some improvements for estimation by moments and can
- use MLE as well as mu/var (-z 3).
-
-(3) add p() estimate.
-
-(4) correct bugs in nrand48, which caused bad sequences for llgetaa.c
-
-(5) -Z number works properly for prss3 and other programs (fixed histogram).
-
-(6) a new program, ssearch3e, is available that uses the same scaling
- routines as prss3 (scaleswe.c). prss3 will save the random
- sequences it generates when the -r file option is given; the
- sequences are in file_rlib. ssearch3e (or ssearch3 or fasta) can
- then do a search on exactly the same sequences that were used by prss3.
-
-A bug reading GCG format compressed DNA databases was fixed.
-
-Fixed a bug that caused query sequence not to be displayed with -m 10.
-
-Simple optimization in dropnfa.c improves performance 10%.
-
->>Sept. 1, 1998
-
-(no version change)
-
-Modified nxgetaa.c to recognize "ACGTX" as nucleotides.
-
->>Sept. 7, 1998
-
- --> v31t12
-
-Added -z 11 - 15, which use shuffled sequences, rather than real
-sequences to calculate statistical estimates. Because a shuffled
-sequence score is calculated for each sequence score, the search
-process takes twice as long. In this first version, codons are not
-preserved during shuffles, so tfasta/x/y shuffles may not be as
-informative as they should be.
-
-Also fix a problem with prss3 shuffles.
-
->>Sept. 14, 1998
-
- (no version change; previous version not released)
-
-Corrected bugs in tfastx3/tfasty3 caused by using the -3 option with
-or without -i. With the bug fixes; "-3" and "-3 -i" work as expected;
-"-3" gives the forward three frames, while "-3 -i" gives the reverse
-three frames.
-
-In addition, tfasta3/tfasta3_t was upgraded to perform the same way
-that tfastx/y3 does - i.e. a search with "-i -3" searches only frames
-4,5, and 6, while "-3" searches only frames 1, 2, and 3.
-
->>Sept. 29, 1998
-
- --> v31t13
-
-Corrected bugs in dropfx.c that were corrected in fasta30 last May,
-but lingered in fasta31. Also included code to ensure that tfastx/y
-alignments against long introns would not overrun the alignment
-buffer. Instead of overrunning the buffer, the message: ***aligment
-truncated *** is displayed.
-
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