[Bioclusters] BLAST 2.2.12 released

Joe Landman landman at scalableinformatics.com
Wed Sep 7 10:00:45 EDT 2005

<forwarded: RPMs will be available soon from 

We are pleased to announce the availability of BLAST 2.2.12. Binaries are
available from the BLAST download page.

Notes for the 2.2.12 release

Bug fixes

     * The megablast -s option was not functioning; fixed in megablast.c
     * Multithreaded megablast was not functioning; fixed in megablast.c
     * Selenocysteine residues were not scored properly in protein
alignments; fixed in blast_kappa.c 1.57 & 1.58, kappa.c 6.62 & 6.63.
     * Ungapped blastpgp was not functioning correctly and was deemed
unnecessary; the -g option was removed in blastpgp.c 6.131.
     * formatrpsdb was not working properly; fixed in formatrpsdb.c 1.18.


     * Megablast, rpsblast, and bl2seq now use the new BLAST engine codebase
by default. This can result in significantly faster searches.
     * Discontiguous megablast is now substantially faster.
     * formatdb can now incorporate taxonomic information into BLAST
databases by using the -T option.
     * fastacmd can now dump accessions by using the -D 3 option.
     * New compositional score adjustment algorithms are implemented in
blastpgp; see Bioinformatics 21:902-911, 2005 for details.

If you have any questions please contact blast-help at ncbi.nlm.nih.gov.

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615

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