DNA/Protein homology search

Maido Remm mremm at tamm.eenet.ee
Mon Feb 9 05:37:16 EST 1998


Hei,

Has anybody written script or program to align gene DNA sequences according
to their protein sequence: I mean it should do the following

1. Query and target are DNA
2. Translate both sequences correctly to protein sequence
3. Align protein sequences
4. Output the same alignment as DNA sequence

I would name it codon alignment. It should have much more sense than
straigth comparision of DNA. I have been told that similar program have
announced here recently, but i was unable to find something like that in
archives. 

Thanks for your time,
Maido Remm
Estonian Biocentre. 




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