Re: [Gmod-gbrowse] How to use draft sequence in the GBrowse_syn?

[Scott C. <sc...@sc...>]

Hi xukai,

What do you have now?  Just the fasta sequences of the contigs?  If
so, all you need to do is create one GFF line for each contig, which
would look something like this:

contig1234  .   contig   1   <length>   .   .    .   Name=contig1234

You can also put the sequence of the contig at the bottom of the GFF
file if you like:

...gff lines...
##FASTA
>contig1234
atgaatagc....

This is fairly easy to do with a short perl script.  If you don't want
to write one yourself, there is a script called gmod_fasta2gff3.pl in
the Chado distribution:

http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/bin/gmod_fasta2gff3.pl?revision=25275&content-type=text%2Fplain

It only relies on BioPerl, so you can download it directly without
getting all of Chado.

Scott


On Thu, Oct 18, 2012 at 5:05 AM, Kai Xu <xuk...@gm...> wrote:
> hey guys,
>
> i am learning how to use the GBrowse_syn to do a comparison between two
> bacillus strains. one of them is complete sequence but the other is a draft
> sequence which contains many contigs. now i have finished the BLAST between
> the two strains and converted the BLAST results to clustalW format. but when
> i import the sequence into GBrowse_syn, as we know that it requires the
> sequence to be GFF3 format. so how can i deal with the draft sequence? can
> anyone give me some suggestions? thanks.
>
> yours,
> xukai
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research