[Bioperl-l] starting out with Boulder

[Jason Stajich]

This is very old documentation, I guess I will try and carve out time for
updating this at some point.

On Tue, 20 Aug 2002, Lincoln Stein wrote:

> I hate to differ, Jason, but if you look at bioperl.pod and search for BLAST,
> the very first thing it does is to tell you to use Bio::Tools::Blast.
> (Actually first it tells you to use Bio::Tools::BPLite, and then it tells you
> to use Bio::Tools::Blast.)
>
> You have to go several more pages into the documentation before you get a
> mention of Bio::SearchIO.
>
> Now, I know that the mailing list word is to use Bio::SearchIO for this, but
> until the official .pod documentation is changed, it is vital that we speak
> with one voice!
>
> Lincoln
>
> =head1 Examples/ Directory
>
> There are many scripts included in the distribution.
> Here are brief descriptions of the scripts in the I<examples/> directory:
> ...
>
> I<examples/BioPerlBlast.pl> - script that takes multiple query sequences
> and queries a database with Blast
>
> I<examples/blast/*pl> - a set of scripts showing how to use Blast.pm.
> Please see L<Bio::Tools::Blast> for more information
>
>
>
> On Tuesday 20 August 2002 04:03 pm, Jason Stajich wrote:
> > NO!
> >
> > Use
> >
> > Bio::SearchIO
> >
> > On Tue, 20 Aug 2002, Lincoln Stein wrote:
> > > Boulder is entirely deprecated.  Use the BioPerl Bio::ToolsBlast module.
> > >
> > > Lincoln
> > >
> > > On Tuesday 20 August 2002 03:27 pm, skw p wrote:
> > > > hello list,
> > > > i have a set of tblastx results i need to parse out. I
> > > > want to use Boulder
> > > > for the job,after making modifications if any needed.
> > > > I have no clue how to get
> > > > started with this package, though!
> > > > the documentation doesnt help me much- is there any
> > > > other online manual
> > > > help etc?
> > > > thanks alot
> > > > skw
> > > >
> > > >
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>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu