[BiO BB] [BLAST-Announce #053] BLAST 2.2.13 released]

Joe Landman landman at scalableinformatics.com
Tue Dec 13 10:59:29 EST 2005



-------- Original Message --------
Subject: [blast-announce] [BLAST-Announce #053] BLAST 2.2.13 released
Date: Tue, 13 Dec 2005 10:53:34 -0500

Notes for the 2.2.13 release

Standalone BLAST 2.2.13 is now available from the BLAST download page.

Major changes include:

     * New engine now available in blastall
     * Statistical parameter change
     * Bug fixes

New engine available in blastall

Blastall now has support for a new version of the BLAST engine that can
be enabled by adding "-V F" to the blastall command-line. This option
will probably be the default in future versions. There are a few
situations where it is very advantageous to use the new engine:

    1. Large word-sizes with a BLASTN search. The new engine uses the
"stride" idea of AGBLAST and this can lead to a considerable speedup for
large word sizes. For a run of a typical mRNA sequence (u00001) with a
word size of 25 the new code runs about twice as fast as the old code.
Note that the AG "stride" has been available in megablast since the
2.2.10 release. This enhancement is platform-independent.
    2. Searching multiple queries at once. The new engine will search
multiple queries by scanning the database once, rather than once for
each query. The speedup will depend upon the queries being searched and
what part of the time is spent scanning the databases vs. actual
computations (e.g., extensions etc.). Typically this feature is most
important if a number of short queries (e.g., mRNA's or EST's) are being
searched with blastn or if a tblastn search is performed. This feature
is partially supported in the old code with the -B option as well as by
megablast.
    3. For very large queries. The memory management (especially during
the dynamic programming phase) has been improved and this may allow
searches with lots of matches or large queries that used to fail to now
run to completion.

Statistical parameter change

Megablast, blastall and bl2seq have until now allowed users to select
arbitrary gap existence and extension penalties for a blastn type
search. This has been convenient for users but has led to the
unfortunate situation that searches with some parameter sets were
significantly overestimating the statistical significance of matches. To
address this problem the proper statistical parameters for a number of
reward/penalty/gap existence/gap extension values have been calculated.

The parameters that might cause an issue here are -r (match reward), -q
(mismatch penalty), -G (gap existence cost), and -E (gap extension
cost). If you do not change these, then nothing will change for you.

Please email blast-help at ncbi.nlm.nih.gov with any questions, bug
reports, or requests for different parameter sets.

Below are listed the supported combinations. Note that above a certain
gap existence and extension penalty any value is permitted, as the
statistics for ungapped searches can be used. These are marked as
"ungapped threshold" below.

For match = 1, mismatch = -4 the supported combinations are:

G  E
-----
1, 2,
0, 2,
2, 1,
1, 1,
2, 2 (ungapped threshold)


match = 2, mismatch = -7 the supported combinations are:

G  E
-----
2, 4,
0, 4,
4, 2,
2, 2,
4, 4 (ungapped threshold)

match = 1, mismatch = -3 the supported combinations are:

G  E
-----
1, 2,
0, 2,
2, 1,
1, 1
2, 2 (ungapped threshold)

match = 2, mismatch = -5 the supported combinations are:

G  E
-----
2, 4,
0, 4,
4, 2,
2, 2,
4, 4 (ungapped threshold)

match - 1, mismatch = -2 the supported combinations are:

G  E
-----
1, 2,
0, 2,
3, 1,
2, 1,
1, 1,
2, 2 (ungapped threshold)

match = 2, mismatch = -3 the supported combinations are:

G  E
-----
4, 4,
2, 4,
0, 4,
3, 3,
6, 2,
5, 2,
4, 2,
2, 2,
6, 4 (ungapped threshold)

match = 1, mismatch = -1 the supported combinations are:

G  E
-----
3, 2,
2, 2,
1, 2,
0, 2,
4, 1,
3, 1,
2, 1,
4, 2 (ungapped threshold)

match = 5, mismatch = -4 the supported combinations are:

G  E
-----
10, 6
8, 6
25, 10 (ungapped threshold)

match = 4, mismatch = -5 the supported combinations are:

G  E
-----
6, 5,
5, 5,
4, 5,
3, 5,
12, 8 (ungapped threshold)


Bug fixes

     * A bug has been fixed in formatdb. This bug occurred when the -o
option was not used, meaning that the FASTA definition lines of the
input file were not parsed, and multiple database volumes were
generated. The bug normally did not become apparent to the user until
the BLAST run at which point the BLAST binary (e.g., blastall) would
produce messages containing "ObjMgrChoice: pointer [0] type [1] not
found".

-- 
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




More information about the BBB mailing list