[BiO BB] [Fwd: [blast-announce] BLAST-Announce #056] BLAST 2.2.15 released]

Joe Landman landman at scalableinformatics.com
Fri Oct 20 08:48:31 EDT 2006

-------- Original Message --------
Subject: [blast-announce] BLAST-Announce #056] BLAST 2.2.15 released
Date: Fri, 20 Oct 2006 08:37:34 -0400

Notes for the 2.2.15 release

BLAST 2.2.15 is now available from the BLAST download page.

Major changes include:

    * BLAST now uses a 28-letter protein alphabet supporting the J
(leucine or isoleucine) and O (pyrrolysine) residues.
    * formatrpsdb will now generate RPS blast databases that assume a
28-letter alphabet. These databases are incompatible with rpsblast
versions older than 2.2.15.
    * blastpgp can now combine the e-value from the alignment with a
p-value determined by the composition to yield a unified e-value that is
ultimately used to evaluate the significance of alignments. This
behavior can be enabled with the -t 1u or -t 2u options.
    * megablast now supports incremental ASN.1 output. This behavior can
be enabled with the -D 4 and -D 5 options.
    * BLAST binaries are now available for Windows XP/2003 x64 edition.
    * blastx searches are now significantly faster for queries exceeding
10kbp in length.
    * seedtop can now perform pattern searches even if the pattern is
considered too likely to occur. This behavior can be enabled with the -f
    * BLAST now natively supports the BLOSUM50 and BLOSUM90 score
    * BLAST now correctly handles databases restricted by gi lists even
if no sequences will be searched.
    * blastall now prints a header for each query even if queries have
been concatenated.

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

Scott D. McGinnis, M.S.

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 or +1 866 888 3112
cell : +1 734 612 4615

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