[Biopython-dev] Fwd: [blast-announce] BLAST 2.2.22 now available

Peter peter at maubp.freeserve.co.uk
Tue Oct 20 11:56:51 UTC 2009

Hi all,

The new NCBI BLAST tools are out now, and I'd only just updated
my desktop to BLAST 2.2.21 this morning!

It looks like the "old style" blastall etc (which are written in C) are
much the same, but we will need to add Bio.Blast.Applications
wrappers for the new "BLAST+" tools (written in C++).

On the bright side, the Biopython tutorial needed updating
anyway to switch from Bio.Blast.NCBIStandalone.blastall(...)
to using Bio.Blast.Applications and subprocess.


---------- Forwarded message ----------
From: mcginnis <mcginnis at ncbi.nlm.nih.gov>
Date: Tue, Oct 20, 2009 at 12:42 PM
Subject: [blast-announce] BLAST 2.2.22 now available
To: blast-announce at ncbi.nlm.nih.gov

BLAST 2.2.22 now available

This release includes new BLAST+ command-line applications.

The BLAST+ applications have a number of advantages over the older
applications and users are encouraged to migrate to the new
applications.  The new applications can be downloaded from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST  These
applications have been built with the NCBI C++ toolkit. Changes from
the last release are listed below.

The older C toolkit applications (e.g., blastall) are still available
at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/
Changes from the last release are listed below.

Please send questions or comments to blast-help at ncbi.nlm.nih.gov

Changes for the BLAST+ applications:

* Added entrez_query command line option for restricting remote BLAST databases.
* Added support for psi-tblastn to the tblastn command line application via
  the -in_pssm option.
* Improved documentation for subject masking feature in user manual.
* User interface improvements to windowmasker.
* Made the specification of BLAST databases to resolve GIs/accessions
* update_blastdb.pl downloads and checks BLAST database MD5 checksum files.
* Allow long words with blastp.
* Added support for overriding megablast index when importing search strategy
* Added support for best-hit algorithm parameters in strategy files.
* Bug fixes in blastx and tblastn with genomic sequences, subject masking,
  blastdbcheck, and the SEG filtering algorithm.

Changes for C applications:

* Blastall was not able to use BLAST databases with only accessions to
format results, this has been fixed.

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