PASSML: combining evolutionary inference and protein secondary structure prediction.
BACKGROUND
Evolutionary models of amino acid sequences can be adapted to incorporate structure information; protein structure biologists can use phylogenetic relationships among species to improve prediction accuracy. Results : A computer program called PASSML ('Phylogeny and Secondary Structure using Maximum Likelihood') has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement. The model is related to that of Dayhoff and co-workers, but we distinguish eight categories of structural environment: alpha helix, beta sheet, turn and coil, each further classified according to solvent accessibility, i.e. buried or exposed. The model of sequence evolution for each of the eight categories is a Markov process with discrete states in continuous time, and the organization of structure along protein sequences is described by a hidden Markov model. This paper describes the PASSML software and illustrates how it allows both the reconstruction of phylogenies and prediction of secondary structure from aligned amino acid sequences.


BACKGROUND
PASSML 'ANSI C' source code and the example data sets described here are available at http://ng-dec1.gen.cam.ac.uk/hmm/Passml.html and 'downstream' Web pages.


BACKGROUND
P.Lio@gen.cam.ac.uk
Liò
P
P
Department of Genetics, University of Cambridge, Cambridge, UK. University of Warwick, UK.
Goldman
N
N
Thorne
J L
JL
Jones3
D T
DT
D000263:Adenylate Kinase / Q000235:genetics; D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D016208:Databases, Factual; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D006801:Humans; D009345:Neisseria meningitidis / Q000235:genetics; D010802:Phylogeny; D017433:Protein Structure, Secondary; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D016415:Sequence Alignment; D012984:Software
D000263:Adenylate Kinase