[Bioperl-l] FYI: interesting stuff in BLAST 2.2.24 release announcement

Dave Messina David.Messina at sbc.su.se
Tue Aug 24 13:00:14 EDT 2010

Here's a link to the manual:

(Is it on the NCBI website somewhere? Strange to have only a downloadable PDF.) The section on the new archive format is on page 27.

It seems like a nice idea to have the flexibility, but I wonder about the time cost of using this format.

One of the big gains from using tab-delimited output is that BLAST doesn't have to do all the post-processing to generate the alignment views. By doing the archive format, which if I understand it correctly is ASN.1, you're always paying the full price in time (and space, for that matter).


On Aug 24, 2010, at 18:17 , Chris Fields wrote:

> FYI,
> Very interesting additions to BLAST+ (archive format).  
> chris
> Begin forwarded message:
>> From: mcginnis <mcginnis at ncbi.nlm.nih.gov>
>> Date: August 24, 2010 10:46:50 AM CDT
>> To: NLM/NCBI List blast-announce <blast-announce at ncbi.nlm.nih.gov>
>> Subject: [blast-announce] Correction: BLAST 2.2.24 release announcement
>> A new version of the stand-alone applications is available.
>> Users are encouraged to use the BLAST+ applications available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
>> This release includes a number of bug fixes as well as new features for the BLAST+ applications:
>> * Introduce BLAST Archive format to permit reformatting of stand-alone BLAST searches with the blast_formatter(see BLAST+ user manual) 
>> * Added the blast_formatter application (see BLAST+ user manual)
>> * Added support for translated subject soft masking in the BLAST databases
>> * Added support for the BLAST Trace-back operations (btop) output format
>> * Added command line options to blastdbcmd for listing available BLAST databases
>> * Improved performance of formatting of remote BLAST searches
>> * Use a consistent exit code for out of memory conditions
>> * Fixed bug in indexed megablast with multiple space-separated BLAST databases
>> * Fixed bugs in legacy_blast.pl, blastdbcmd, rpsblast, and makeblastdb
>> * Fixed Windows installer for 64-bit installations
>> BLAST+ applications, as well as the legacy C applications (e.g. blastall), may be downloaded from http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
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