[Biopython-dev] Fwd: New Biopython (sub)module?

Cyrus Maher michael.maher at ucsf.edu
Mon Aug 19 19:24:04 UTC 2013

Hi everybody!!-

My name is (Michael) Cyrus Maher, and I'm a PhD student at UCSF in the lab
of Dr. Ryan D. Hernandez (http://bts.ucsf.edu/hernandez_lab/)...

I am writing because I'm interested in submitting a new Biopython module.
Since this is likely a one-time event, the wiki recommends proceeding
through a developer. After speaking with Peter Cock, he recommended that I
open things up for discussion on the mailing list.

Attached is a draft that describes a new method, termed MOSAIC, which
integrates multiple sequence alignments from an arbitrary number number of
sources. We show that it greatly increases the number of orthologs that we
are able to detect while maintaining or improving functional-,
phylogenetic-, and sequence identity-based measures of ortholog quality.

Code and documentation may be found here:


Looking forward to hearing what you think!


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