gbrowse is a genome browser, but can it also be good as trascriptome browser

[Tatamil Tatamil]

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Hello gbrowse team, I understand that gbrowse was designed as a genome browser, but can it also be good for displaying separate gene transcripts. I would like to display >3000 gene transcripts in a graphical representation (e.g. representing splicing variants of the gene in a graphical way, and alignments). The user should be able to click on, or type a name of a gene, and get such graphical display. I would apritiate your answer, and suggestions Tal

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[Scott Cain-4]

Hi Tal,

Yes, you can use GBrowse as a transcript browser.  GBrowse doesn't care what the coordinate system is, so you can use the cDNA/mRNA as the coordinate system, and display features on the transcript like protein motifs and SNPs, as well as exon structure.  There are even a few groups that use GBrowse as a protein browser, using amino acid residues as the coordinate system (SGD's proteome browsers comes to mind).

Scott

On Fri, Oct 23, 2009 at 9:29 AM, Tatamil Tatamil <taltamil@...> wrote:

Hello gbrowse team, I understand that gbrowse was designed as a genome browser, but can it also be good for displaying separate gene transcripts. I would like to display >3000 gene transcripts in a graphical representation (e.g. representing splicing variants of the gene in a graphical way, and alignments). The user should be able to click on, or type a name of a gene, and get such graphical display. I would apritiate your answer, and suggestions Tal

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--
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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


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