[Bioperl-l] StandAloneBlast & BLAST+

[Chris Fields]

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