Clustal (Gap penalty)

[Wagner Fontes]

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





.