[Bioperl-l] clustalw output format

[Jason Eric Stajich]

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.

IbatANS   EKVRVSWAVFCEPPKEKIILQPLPETVSEADPPRFPPRTFAQHIKHKLFRQTDQEGADTP
IpurpANS  EKVRVSWAVFCEPPKDKILLQPLPETVSEAEPPRFPPRTFARHIKHNLFRQSDQEAAHTP
          ***************:**:***********:**********:****:****:***.*.**

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

-jason
-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu