[Gmod-help] Re: [Gmod-gbrowse] GBrowse for Viral genomes

[jo sequeira]

Hi Dave,
Thanks for the reply. 
Yes you're right in that the virus genomes are too many in number and are also segmented. So each Influenza virus is made up of 8 segments, We have over 76,000 segment sequences for Influenza and would like to be able to view each of these in GBrowse. Right now we have concatenated all 8 segments of a few selected viruses and display them as a complete sequence. It's hard to do the same for all the remaining ones. So I was trying to figure out if GBrowse can display segmented genomes and in so many numbers. Thanks again.

Even the word "Impossible" says "I m Possible" and "Prayer"  tagged with"Faith" makes all things possible !

--- On Tue, 6/2/09, Dave Clements, GMOD Help Desk <gmodhelp at googlemail.com> wrote:

From: Dave Clements, GMOD Help Desk <gmodhelp at googlemail.com>
Subject: Re: [Gmod-gbrowse] GBrowse for Viral genomes
To: "jo sequeira" <jolovesjo at yahoo.com>
Cc: gmod-gbrowse at lists.sourceforge.net
Date: Tuesday, June 2, 2009, 9:39 AM

Hi Jo,

I don't have enough knowledge of viral genomics to fully understand
your question, but I think I get the gist of it.

GBrowse can display anything from high quality reference genomes to
unmapped EST collections.  What changes between the two is how you
search for the data.  If you have 20 well defined chromosomes, you can
have a pull-down listing all chromosomes.  If you have 10,000 ESTs a
pull down won't work and you have to access the data via name
searching, BLAST, or from external links (e.g., an EST page).

I'm guessing that viral sequences are more like the EST case then the
reference case.

Hope this helps,

Dave C


On Mon, Jun 1, 2009 at 7:31 AM, jo sequeira <jolovesjo at yahoo.com> wrote:
> Is it possible to view large number of virus sequences on GBrowse. Since
> viral genomes can be segmented and have fewer proteins but several
> thousand's  of sequences, (unlike bacterial genomes that can have thousands
> of genes and fewer genomes), can GBrowse handle those numbers of viral
> genomes?
> Thanks
>
> Even the word "Impossible" says "I m Possible" and "Prayer"  tagged
> with"Faith" makes all things possible !
>
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Learn more about GMOD at:
  SMBE: http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
  Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
  AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration



      
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