Deletions in protein sequence alignments

Mark Cohen cohen at
Fri May 15 00:49:59 EST 1992

Hi all,

I have a question regarding deletions in sequence alignments.  Most alignment
programs use the formula ak+b to score an alignment of length k with b as the
fixed gap penalty and a as the incremental gap penalty.  What are the default
values these parameters take in the common commercial alignment packages.  Is
there a consensus about what these values should be or do people simply use
what works.

Thanks for any help people can give.
Mark Cohen
cohen at

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