Mapping HiSeq to Proteins

[DrS]

I've got a project with a tight deadline that will include needing to map some RNASeq data to a reference.

There is a reference transcriptome "published", but only the protein sequences are available, not the DNA.

Does anyone know of any tools that will let me map my fastq files to a protein reference? I've been searching around, but might get an answer faster this way

Right now I'm thinking (dreading?) I may need to do a fastq-to-fasta and use exonerate.

Thanks for any ideas.

[anth]

Why not perform a de novo assembly with your RNAseq data instead?

[DrS]

That is running but will likely take a couple of days, which is part of why I was looking for an alternative approach.

Plus now I'm simply curious - is there a tool out there that will let you make RNASeq reads to a proteome?

[Richard Finney]

Check out blat.
Blast can do it , too.

*at least I think they do*