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.