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Re: GBrowse for Viral genomes
by Dave Clements, GMOD Help Desk
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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@...> 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:
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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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looking to deploy the next generation of Solaris that includes the latest
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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@...> 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 !
>
> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals.
> Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
--
Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
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
------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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