Extracting coding sequences from genomic scaffolds

[RNAddict]

I have a list of sequences (cDNA) that I want to find in many different organisms. I have obtained genomic scaffolds for these organisms from various locations.

I BLAST my cDNA sequences against the genomic scaffolds and find the best reciprocal BLAST hits. The problem is that the hits are broken up (presumably by introns in the genomic scaffolds). Is there an efficient method or tool for extracting just coding sequences from a genomic scaffold?

thanks.

[shunyip]

Maybe you can filter your genomic scaffolds into coding-genes-only by using gene annotation files from UCSC.

[N311V]

I'm not sure exactly what you're trying to do. If it's to extract the sequence of the BLAST hit from the scaffolds it sounds like a job I'd do with perl.