DNA -> Protein comparison

All,

I was wondering if anyone out there had produced a protocol that would allow one to compare two nucleic acid sequences and then determine if there were any differences at the protein level.

For example in the alignment below:

Align.JPG

Not only do I want to know that I have an A to C mutation at position 5 of my reference nucleotide sequence but also that I have a Lys to Thr mutation at position 2 of the reference protein sequence. There are a few issues around truncating the query (which can be a forward or reverse match), whether to do the alignment before or after translation and maintaining the frame information that mean it may be a little tricky so thought I’d check whether such a beast existed anywhere within the Accelrys family vaults.

Thanks

Rich