[Bioperl-l] StandAloneBlastPlus

Mark A. Jensen maj at fortinbras.us
Sun Sep 26 20:43:15 EDT 2010

Hi Hans-- Dave is right; you'll need both the new blast+ as well as the latest BioPerl trunk code. Get it by doing both of the following:

git clone http://github.com/bioperl/bioperl-live.git
git clone http://github.com/bioperl/bioperl-run.git

(i.e., you need the latest core and run distributions). To install, see http://www.bioperl.org/wiki/Installing_BioPerl

cheers MAJ

Mark A. Jensen, PhD
Senior Consultant
Fortinbras Research

>-----Original Message-----
>From: Dave Messina [mailto:David.Messina at sbc.su.se]
>Sent: Sunday, September 26, 2010 12:11 PM
>To: 'Waldenmaier, Hans Eugene'
>Cc: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] StandAloneBlastPlus
>Hi Hans,
>> I think the real problem is the "cannot find path to Blastall.
>Yes. But it sounds like you're trying to use the Bio::Tools::Run modules for the old Blast, not Blast+. Blast+ doesn't have a blastall executable, it has blastn, blastp, etc.
>See http://www.bioperl.org/wiki/HOWTO:BlastPlus for example code.
>Also, you probably need to upgrade your BioPerl installation. I'm pretty sure BioPerl 1.5.2 doesn't have the Blast+ code in it.
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org

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