Clustal (Gap penalty)

Wagner Fontes WAGNERF at BRUNB.BITNET
Thu Sep 2 15:40:09 EST 1993


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?

Thanks,

Wagner Fontes(WAGNERF at BRUNB.BITNET)
Brazilian Center of Protein Sequencing
Biochemistry and Protein Chemistry Lab.
University of Brasilia
Brasilia - Brazil





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