To: raz@cbs.dtu.dk From: Jarmo Schrader Subject: Modified RevTrans Date: Sat, 10 Sep 2005 18:13:23 +0200 Hej Rasmus, I just discovered your RevTrans script, it was an enormous help because I have to prepare DNA alignments for some twenty gene families with totally over 500 sequences and not much time to do that. But in order to work for me, I had to modify the code a bit. Let me explain: I have ready-made, sometimes manually improved protein alignments but in most cases I did not use the full protein but only one or several domains. Alignment is often very poor at the ends of proteins. RevTrans, on the other hand, assumes the protein sequence is full length. So I inserted some code to find the starting position of a truncated protein sequence within its coding DNA and start reverse translation from there. I fixed RevTrans in a quick and dirty way to do what I want, as I am not much of a programmer and have never seen python code before, the result is not very pretty. But maybe you are interested in including an option to use truncated protein sequences as an input and integrate it properly into the code. I am sending you my version so you can see, how I solved the problem. Thanks again for a very helpful script, Jarmo -- Jarmo Schrader ZMBP, Developmental Genetics Auf der Morgenstelle 3 72076 Tûbingen Germany