Bayesian search of functionally divergent protein subgroups and their function specific residues.
BACKGROUND
The rapid increase in the amount of protein sequence data has created a need for an automated identification of evolutionarily related subgroups from large datasets. The existing methods typically require a priori specification of the number of putative groups, which defines the resolution of the classification solution.


RESULTS
We introduce a Bayesian model-based approach to simultaneous identification of evolutionary groups and conserved parts of the protein sequences. The model-based approach provides an intuitive and efficient way of determining the number of groups from the sequence data, in contrast to the ad hoc methods often exploited for similar purposes. Our model recognizes the areas in the sequences that are relevant for the clustering and regards other areas as noise. We have implemented the method using a fast stochastic optimization algorithm which yields a clustering associated with the estimated maximum posterior probability. The method has been shown to have high specificity and sensitivity in simulated and real clustering tasks. With real datasets the method also highlights the residues close to the active site.


BACKGROUND
Software 'kPax' is available at http://www.rni.helsinki.fi/jic/softa.html
Marttinen
Pekka
P
Department of Mathematics and Statistics, PO Box 68, 00014 University of Helsinki, Finland. pekka.marttinen@helsinki.fi
Corander
Jukka
J
Törönen
Petri
P
Holm
Liisa
L
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D001185:Artificial Intelligence; D001499:Bayes Theorem; D017124:Conserved Sequence; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D000596:Amino Acids; D011506:Proteins