[Bioperl-l] clustalw output format

Jason Eric Stajich jason@cgt.mc.duke.edu
Mon, 15 Oct 2001 10:00:41 -0400 (EDT)

In a Clustal alignment what do the '.' and ':' signify - I assume
conservative transitions either by hydrophobicity and charge or from
BLOSUM matrices, not sure how I would calculate them though without
knowin exactly what they code for.

I'd like to generate this line when displaying an alignment from
AlignIO::clustalw so need to know what each means.  I have implemented
just the * right now since that is an easy calculation. This is done by
adding a function to SimpleAlign called match_line and is utilized by the
AlignIO::clustalw module.


I am also looking to add NIBF-PIR format to the AlignIO family.

Jason Stajich
Duke University