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BLAST Software Update (Was: BLAST segmentation faults)

Warren Gish gish at host.nlm.nih.gov
Thu Apr 15 23:50:40 EST 1993

Source code for improved versions of the BLAST application programs is
available for anonymous ftp retrieval on ncbi.nlm.nih.gov ( in four
compressed "tar" files beneath the /pub/blast directory.  The posted source
code now corresponds to the applications in use on the NCBI BLAST servers.
The current version numbers and brief program descriptions are:

   BLASTP  1.3.2  (protein query vs. protein database)
   BLASTN  1.3.0  (nucleotide query vs. nucleotide database)
   BLASTX  1.3.2  (translated nucleotide query vs. protein database)
   TBLASTN 1.3.0  (protein query vs. translated nucleotide database)

Source code for the previous 1.2.x versions of these programs is archived
beneath the directory /pub/blast/archive.

Of greatest importance in the new versions is that BLASTP and (optionally)
BLASTX exhibit increased sensitivity, owing to the consistent use of a much
lower cutoff score.  And all of the BLAST programs, not just BLASTP and BLASTX,
are more selective than before, due to a more accurate procedure of Stephen
Altschul's design for estimating Poisson P-values in the case of multiple HSPs.

In addition to being able to employ multiple processors on Silicon Graphics
PowerIRIS platforms, multithreaded versions of the programs can now be built
under SunSoft Solaris 2.2, with support present but untested for threads under
Digital OSF/1.  Both shared memory and memory-mapped files are supported.
The database file formats are unchanged from the 1.2 versions.

Most of the new features in the BLAST programs remain to be documented in the
manual page, however considerable detail and instructions are provided in the
file /pub/blast/HISTORY.

Re: the bug in TBLASTN 1.2 described by Gary Williams.  A fix for it was posted
in the ftpable source code several weeks ago.  This bug would arise when a
database sequence less than 3 nucleotides (1 codon) in length was encountered.

Warren Gish
gish at ncbi.nlm.nih.gov

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