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

[Chris Fields]

It's probably more applicable from the viewpoint of a cluster admin who would want to add the flexibility of having a single archive and allowing any format (as opposed to re-running the analysis). I'm just wondering if there is anything to glean there for possible alignment archiving purposes (ala SAM/BAM), but if it's ASN.1, likely not.

chris

On Aug 24, 2010, at 12:00 PM, Dave Messina wrote:

> Here's a link to the manual:
> ftp://ftp.ncbi.nlm.nih.gov//blast/executables/blast%2B/2.2.24/user_manual.pdf
> 
> (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).
> 
> 
> 
> Dave
> 
> 
> 
> 
> 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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