[Bioperl-l] StandAloneBlast & BLAST+

Chris Fields cjfields at illinois.edu
Wed Jul 28 08:56:41 EDT 2010


I'll be working on a 1.6.2 release very soon (had a slight delay due to problems with circular seqs).  But BioPerl-Run and others will also be released as well.
On Jul 28, 2010, at 12:14 AM, Matthew Laird wrote:

> Thanks, good to know.  Is there an estimate when it might be stable in the tarball for bioperl-run?
> 
> I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request.  And not everyone who tries to install our software is as computationally inclined...
> 
> Thanks for the work guys, we couldn't do it without Bioperl at the core.
> 
> On 10-07-27 06:29 PM, Chris Fields wrote:
>> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote:
>> 
>>> Good day,
>>> 
>>> Hopefully a quick (and non-repeated) question.  I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+?
>>> 
>>> Unfortunately the + sign in the name makes it a little hard to google. :)
>>> 
>>> Thanks.
>> 
>> Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus).  I've used it quite a bit locally, and am trying to get our cluster switched over to it as well.  It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;>
>> 
>> Note that it is available in bioperl-run, not bioperl-live.  Also best to get the github version for this.  There is also a bit of online documentation on this:
>> 
>> http://www.bioperl.org/wiki/HOWTO:BlastPlus
>> 
>> chris




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