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-   -   Finding Exon-Intron Junctions without a reference genome (http://seqanswers.com/forums/showthread.php?t=11488)

brachysclereid 05-19-2011 11:52 AM

Finding Exon-Intron Junctions without a reference genome
 
Hi,
I'm trying to find intron-exon junctions in assembled transcriptome data without a reference genome. Does anyone know of a tool that can do this?

krobison 05-19-2011 06:27 PM

In general this is an underdetermined problem; most of the information for making the splice lies in the introns. There is a weak signal left behind, but not much.

Your best bet is probably to compare your assembled RNA to the closest relative you can find with this information.

brachysclereid 05-19-2011 07:00 PM

Finding Exon-Intron Junctions without a reference genome
 
Thanks for the advice. I'll try using a relative.

DZhang 05-22-2011 06:21 AM

Hi,

You may try Cufflinks or Scripture to let the software figure out the intron/exon junctions for you.

Douglas
www.contigexpress.com


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