[Bioperl-l] StandAloneBlast & BLAST+

Matthew Laird lairdm at sfu.ca
Wed Jul 28 01:14:05 EDT 2010


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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