Align genomic DNA to cDNA reference

[Grit]

Hi,

this is a great forum so I wonder if someone could help. In a former project we generated cDNA sequences which were aligned to several hundred thousand contigs. Now I have genomic sequences from 454 and would like to align the gDNA 454 reads to the cDNA reference contigs. So I need to allow gaps in the reference sequence. Is there a tool that can do this or do I need a de novo assembly of my gDNA reads and then align the assembled reads to the cDNA contigs?

Many thanks
Grit

[flxlex]

Moved to a more appropriate forum.

By way of an answer, I would suggest if you have sufficient coverage - to assemble the gDNA reads first, then map, for example using a tool like exonerate.

[Grit]

Thanks for your suggestion! Meanwhile I did it that way ;-)