[Bioperl-l] StandAloneBlast & BLAST+

Mark A. Jensen maj at fortinbras.us
Wed Jul 28 00:51:03 EDT 2010


>is not backward compatible with StandAloneBlast code, which is a feature, not a 
>bug ;>

If that's not the nicest thing anyone's ever said....

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Matthew Laird" <lairdm at sfu.ca>
Cc: <bioperl-l at bioperl.org>
Sent: Tuesday, July 27, 2010 9:29 PM
Subject: Re: [Bioperl-l] StandAloneBlast & BLAST+


> 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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