Reciprocal Blast With Multiple Contigs Per Gene

[jwhittall]

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