[Bioperl-l] Bioperl-l Digest, Vol 89, Issue 19

bv s gandipalem at gmail.com
Tue Sep 28 00:09:06 EDT 2010


Dear Sir/Madam,

Any one can tell how to use the make_primers.pl script?
What is Coordination file?

Regards
Suresh
Scholar,
National Bureau Of Plant Genetic Resources,
New Delhi.


On Mon, Sep 27, 2010 at 9:30 PM, <bioperl-l-request at lists.open-bio.org>wrote:

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> Today's Topics:
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>   1. Re:  StandAloneBlastPlus (Dave Messina)
>   2. Re:  StandAloneBlastPlus (Mark A. Jensen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 26 Sep 2010 18:11:54 +0200
> From: Dave Messina <David.Messina at sbc.su.se>
> Subject: Re: [Bioperl-l] StandAloneBlastPlus
> To: "Waldenmaier, Hans Eugene" <waldenhe at muohio.edu>
> Cc: "bioperl-l at bioperl.org" <bioperl-l at bioperl.org>
> Message-ID: <5A561A87-A3A3-4CEB-A57E-B719ECFF75F0 at sbc.su.se>
> Content-Type: text/plain; charset=us-ascii
>
> 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.
>
>
>
> Dave
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 27 Sep 2010 00:43:15 +0000
> From: "Mark A. Jensen" <maj at fortinbras.us>
> Subject: Re: [Bioperl-l] StandAloneBlastPlus
> To: "Dave Messina" <David.Messina at sbc.su.se>,   "Waldenmaier, Hans
>        Eugene" <waldenhe at muohio.edu>
> Cc: bioperl-l at bioperl.org
> Message-ID: <W479062635438381285548195 at webmail34>
> Content-Type: text/plain; charset="us-ascii"
>
> 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
> http://www.fortinbras.us
>
> >-----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.
> >
> >
> >
> >Dave
> >
> >
> >_______________________________________________
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> >Bioperl-l at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
>
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>
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> End of Bioperl-l Digest, Vol 89, Issue 19
> *****************************************
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