Bioperl: A greedy consensus builder

Ruediger Hornig
Thu, 5 Aug 1999 11:57:42 +1000

Mike Cariaso ( wrote:

> To scratch an itch I've built a small object which ISA
> Bio::UnivAln.
> It has a single method 'greedy' which constucts a consensus
> sequence using a
> somewhat different method. The approach does ignores alignment
> gaps that are
> before (or after) the first (last) non-gap of a row. An example
> may explain it
> more clearly.

While we are at collecting methods for the alignment object...

I have written something which may be useful for working with
protein sequence alignments. The UnivAln->consensus method
returns identity, while I was interested in homology (eg.
V|I|A|L). So if identity of a column does not make the threshold,
but the residues with a certain property do, the property will be


!SP~F is the 0.75 consensus with ! aliphatic and ~ acidic. If
someone is interested in this type of consensus, or in separate 
identity and homology methods in that
context, I'm happy to contribute that.


Dr Rüdiger Hornig
Computational Molecular Biology And Drug Design
Department For Biochemistry And Molecular Biology
Australian National University, Canberra 0200, Australia
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