Clustal (Gap penalty)

higgins at embl-heidelberg.de higgins at embl-heidelberg.de
Mon Sep 6 11:30:09 EST 1993

In article <9309021947.AA01103 at net.bio.net>, WAGNERF at BRUNB.BITNET (Wagner Fontes) writes:
> Hi,
> I'm trying to align peptides using Clustal V, but found a problem:
> With a low gap penalty, to allow the peptide to be inserted anywhere
> in the sequence, the software inserts long gaps IN the peptide.
> Is there a way to increase the gap penalty only for the internal gaps,
> allowing long gaps at the beginning and/or end of the sequence?
All gaps in clustal v are penalised identically which does look bad when
aligning sequences of greatly different lengths.  This is due to the 
dynamic programming algorithm I used (Myers and Miller, CABIOS, 1988)
which is very memory efficient but which is VERY complicated to modify
(e.g. to penalise end gaps differently or not at all).  I do have a fix
(have had for a year) but have not yet had time to document or debug it
properly.  I hope to release a version with this option soon.  In the meantime,
yes, PILEUP in the GCG package does allow end gaps to be unpenalised.  

So, sorry about the messy ends!  You can always align the sequences manually:-).

Des Higgins

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