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Old 07-21-2010, 01:20 PM   #1
jwhittall
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Location: Santa Clara, CA

Join Date: Aug 2009
Posts: 2
Default Reciprocal Blast With Multiple Contigs Per Gene

Dear SeqAnswers,

I'm assembling a transcriptome de novo and trying to use reciprocal blast to increase my confidence in contig identification. Velvet/Oases produces multiple contigs that blast to the same reference (usually in non-overlapping portions of the gene). Taking the top hit in a reciprocal blast means I lose alot of these contigs and my % coverage for each gene plummets. Any tips on how to do reciprocal blast when multiple contigs blast to the same gene?

Thanks,

Justen
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