DNA/Protein homology search

Burkhard Morgenstern morgenst at gsf.de
Tue Feb 10 09:38:43 EST 1998

Maido Remm wrote:
> 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.


I have written an alignment program that does exactly
what you are looking for. It is called DIALIGN. 

Executables for various UNIX platforms (including LINUX)
are available at


Hope this helps

  Burkhard Morgenstern

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