Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German conference on bioinformatics 2009 P-157, 211-220 (2009).

Gesellschaft für Informatik, Bonn

Copyright © Gesellschaft für Informatik, Bonn


Maximum likelihood estimation of weight matrices for targeted homology search

P. Menzel , J. Gorodkin and P. F. Stadler


Genome annotation relies to a large extent on the recognition of homologs to already known genes. The starting point for such protocols is a collection of known sequences from one or more species, from which a model is constructed - either automatically or manually - that encodes the defining features of a single gene or a gene family. The quality of these models eventually determines the success rate of the homology search. We propose here a novel approach to model construction that not only captures the characteristic motifs of a gene, but are also adjusts the search pattern by including phylogenetic information. Computational tests demonstrate that this can lead to a substantial improvement of homology search models.

Full Text: PDF

Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-251-2

Last changed 04.10.2013 18:29:31