[Gmod-help] RE: [Gmod-gbrowse] Gbrowse_syn alignments

[Rytsareva, Inna (I)]

Hello.

Dave, your idea is cool, but I guess in this case I don't have to use
GBrowse_syn, I need only Gbrowse. I was searching a lot for an
additional documentationv what Gbrowse-syn does and unfortunately I
didn't find any information about the alignment table and columns "seq1"
and "seq2". I'm wondering, what are they for? Maybe it's a way to
display alingment in "ATCG". In WormDatabase samples those columns are
empty and I don't understand how I can use them in my dataset as well as
I have those alignments. Any ideas?


Inna Rytsareva
Discovery Information Management
Dow AgroSciences
Indianapolis, IN 
317-337-4716

-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Monday, June 15, 2009 7:16 PM
To: Rytsareva, Inna (I)
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] Gbrowse_syn alignments

Hi Inna,

I'm on really thin ice here, but I will give it a try.  My answer is
based on my knowledge of GBrowse, rather then on GBrowse_syn per se.

The segments glyph (and probably others) allow you to display the
nucleotide letters and mismatches when you are zoomed in.  See
http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/d
ocs/tutorial/tutorial.html?pathrev=stable#adding_dna_to_alignments

However, I suspect that you'll have to do a LOT of extra work to
define the alignments in GFF3 format (assuming you know what the base
to base alignments are).  Or, this may be easy, and I just don't know
how.  :-(

Anybody else have ideas?

Thanks,

Dave C.


On Mon, Jun 15, 2009 at 9:30 AM, Rytsareva, Inna (I)<IRytsareva at dow.com>
wrote:
> Hello.
>
> How can we get alingments in Gbrowse_syn in the letters for each
synteny
> hit?
>
> Inna Rytsareva
> Discovery Information Management
> Dow AgroSciences
> Indianapolis, IN
> 317-337-4716
>
>
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