[Bioperl-l] Using primer3

[Mike Muratet]

Thanks to all.

I did get latest version installed.

Cheers

Mike

----- Original Message -----
From: "Rob Edwards" <redwards at utmem.edu>
To: "Shawn Hoon" <shawnh at fugu-sg.org>
Cc: "Mike Muratet" <mike.muratet at torchtechnologies.com>;
<bioperl-l at bioperl.org>
Sent: Tuesday, July 08, 2003 11:15 PM
Subject: Re: [Bioperl-l] Using primer3


> The latest version of this is in
http://www.salmonella.org/bioperl/nucleotide_analyses.tgz and has some minor
fixes from the earlier versions.
>
> Also included are several other modules that Heikki has been improving. I
don't know if Heikki has changed anything in Run::Primer3, but I suspect so!
>
> If so - I'd include that module. If not - go for it.
>
> Mike, if you just want to get Primer3 running, this will do it for you,
and there is an example script that will let you fill in any options that
you need. You'll just need to install these manually.
>
> Rob
>
>
>
>
>
> On Wed, Jul 09, 2003 at 09:32:06AM +0100, Shawn Hoon wrote:
> >
> > On Tuesday, July 8, 2003, at 02:26  AM, Mike Muratet wrote:
> >
> > > Greetings
> > >
> > > I'm trying to sort out running the primer3 methods in bioperl 1.2.1
> > > (the latest stable, isn't it?).
> > >
> >
> > bioperl 1.2.2 is just out available at:
> > http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz
> >
> > bioperl-run is available at:
> > http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz
> >
> >
> > > I see  by the README in Bio/Tools/Run that this is a separate branch,
> > > but I don't see at www.bioperl.org or CPAN where it can be downloaded.
> > > (There is no Run::Primer3 that I can see in the directory.)
> > >
> > > I've looked through the wikis and searched the web, but I can't figure
> > > out how to use it. I know it's a simple answer, could someone clue me
> > > in?
> > >
> >
> > Currently Primer3 has no wrapper in bioperl-run. However I managed to
> > dig up an April Email by Rob
> > that has a link to some modules that he has written for working with
> > Primer3.
> >
> > http://www.salmonella.org/bioperl/primer3_v0.3.tgz
> >
> > Rob I can integrate this with bioperl-run if its okay with you.
> > Are you still having problems with the WrapperBase I/O handling?
> >
> > cheers,
> >
> > shawn
> > .
> >
> > > Thanks
> > >
> > > Mike_______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
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