Clustal (Gap penalty)

Doug Eernisse Doug_Ee at um.cc.umich.edu
Fri Sep 3 00:43:16 EST 1993

In article <9309021947.AA01103 at net.bio.net> Wagner Fontes, 
>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?

I think this is a general problem for multiple sequence alignments
in which the sequences are poorly conserved or contain missing
data near some of their ends. We need algorithms that allow anchoring 
of portions of the alignment. Is there a way you can artificially
make the ends more highly matching (temporarily) for the purpose
of matching the central portions, then remove the central portion
back to the unmodified alignment? This problem is why I have
never gotten very far with a nonmanual approach to aligning
mixtures of partial and complete 18S rRNA sequences.

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