NCBI toolkit and binaries

Tom Madden madden at corin.nlm.nih.gov
Tue May 11 15:33:54 EST 1999

A new release of the NCBI toolkit, as well as executables for BLAST,
Sequin, and Entrez is now available on the NCBI FTP site at

A previously announced, support for Win16 and SunOs has been dropped.

Release notes for BLAST are below.

Notes for 2.0.9 release:


1.) two new options have been added to blastall: to produce output in HTML and
to search a subset of the database based upon a list of GI's.  Please see
the options section for full information.

2.) two new options have been added to blastpgp: to produce HTML output and to
produce an ASCII version of the PSI-BLAST Matrix.  Please see the options 
for more information.

3.) formatdb has a new option to allow specification of a 'base' name.  see the 
section for full details.

4.) it is possible to mask only during the phase when the lookup table is being 
but not during the extensions.  See the options section for full details.

Bug fixes:

1.) a problem that occurred when too many HSP's aligned to the same part
of the query from one database sequence has been fixed.

2.) a problem that caused seedtop to not perform pattern-matching for DNA
sequences has been fixed.

3.) the number of HSP's saved for ungapped BLAST and tblastx is now limited to
200 to prevent problems with memory and speed.

4.) a missing thread join that caused problems under DEC Alpha has been added.

5.) a formatting problem with the database summary at the beginning of the
BLAST output (if multiple databases totaling over 2 Gig) has been fixed.

6.) a bug in formatdb that caused a core-dump if the total number of sequences 
was an
exact multiple of 100000 was fixed.

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