New NCBI toolkit and new BLAST binaries

Tom Madden madden at ncbi.nlm.nih.gov
Tue Feb 1 17:17:28 EST 2000

A new version of the NCBI toolkit and new BLAST binaries have
been posted to the NCBI FTP site.  The toolkit is available at
ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/ and the BLAST binaries 
are available at ftp://ncbi.nlm.nih.gov/blast/executables/

This release includes source code for vecscreen (in the 
demo directory). This program is a stand-alone version 
of the VecScreen system for identifying segments of a 
nucleic acid sequence that may be of vector origin (see 
www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html). The 
vecscreen program uses the UniVec or UniVec_Core 
databases which are available at 

Notes for BLAST 2.0.11 release:


1.) Optimizations were contributed by Chris Joerg of COMPAQ.  These changes
reduce the number of cache misses, unroll loops, and make some instructions
unnecessary.  These improvements can speed up BLAST for long sequences

2.) A database is now only memory-mapped while being searched.  If multiple 
are searched and the total exceeds the allowed memory-map limit this allows
all databases to be searched as memory-mapped files.  If a database cannot
be memory-mapped it is read as an ordinary file, rather than causing an error.

Bug fixes:

1.) Formatdb was fixed to correct a problem with FASTA string identifiers under 

2.) Blastpgp was fixed to prevent a core-dump under LINUX

3.) BLASTN was found to miss some hits near the expect value cutoff.  This has 


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