[Gmod-ajax] Define boundary in DNA Fasta sequence

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[Gmod-ajax] Define boundary in DNA Fasta sequence

Swapnil Nagar
Hi,

I have successfully put the DNA sequence in the Jbrowse. We were hoping that like we define the gene boundary for Mrna, Can we do same for the DNA (fasta sequence)? It would be really nice if jbrowse enable us to highlight the biological classes(5' UTR, 3'UTR, exon, intron, etc) in different color.

Thanks,

Swapnil Nagar

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Re: Define boundary in DNA Fasta sequence

Mitch Skinner
On 07/22/2010 12:06 PM, Swapnil Nagar wrote:
> I have successfully put the DNA sequence in the Jbrowse. We were hoping that like we define the gene boundary for Mrna, Can we do same for the DNA (fasta sequence)? It would be really nice if jbrowse enable us to highlight the biological classes(5' UTR, 3'UTR, exon, intron, etc) in different color.
>    

I'm sorry, but I don't understand what you're asking.  Are you talking
about adding some sort of highlighting to the DNA track?  If that's the
case, I don't see how that would work since there's (currently) only one
DNA track but there can be multiple distinct overlapping mRNAs with
differing definitions of what regions are UTRs or exons or introns.  
Your lab works with eukaryotes, right?

Or maybe you have something entirely different in mind?  Could you
elaborate, and maybe give a specific example?

Mitch

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