[Gmod-help] GBrowse for metagenomics multi-fasta contig

[Lincoln Stein]

I agree with Scott. The software scales well to many short contigs.

Lincoln

On Fri, Apr 11, 2008 at 12:05 PM, Scott Cain <cain.cshl at gmail.com> wrote:

> Hello Wenhan,
>
> I'm cc'ing this email to the gbrowse mailing list.
>
> There is no reason that I can think of that it couldn't be used with
> short contigs--there are groups that use it for proteins and their
> features/domains, and those are certainly going to be shorter than
> typical metagenomic contigs.
>
> Scott
>
> On Fri, 2008-04-11 at 11:51 -0400, Wenhan Zhu wrote:
> > Dear Gmod team,
> >
> > Recently, I started to use GBrowse and found it very useful. I have a
> > quick question:
> >
> > I understand that the genome browser is designed to be used for a long
> > stretch of sequence(a complete sequenced genome).
> >
> > I am wondering:
> > The new metagenomic sequences become popular nowadays. The dataset
> > usually has thousands of contigs, each one has 1-2kb short sequences.
> > Is there any resources that can accomodate GBrowse for this type of
> > dataset?
> >
> > Thank you so much,
> > Best regards,
> >
> > Wenhan
> > --
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
>
>


-- 
Lincoln D. Stein
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