UNSPECIFIED (1998) PASSML: combining evolutionary inference and protein secondary structure prediction. BIOINFORMATICS, 14 (8). pp. 726-733. ISSN 1367-4803

Full text not available from this repository.

Abstract

Motivation: 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: a 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.

Item Type:	Journal Article
Subjects:	Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QD Chemistry T Technology > TP Chemical technology Q Science > QH Natural history > QH301 Biology Q Science > QA Mathematics
Journal or Publication Title:	BIOINFORMATICS
Publisher:	OXFORD UNIV PRESS
ISSN:	1367-4803
Date:	1998
Volume:	14
Number:	8
Number of Pages:	8
Page Range:	pp. 726-733
Publication Status:	Published
URI:	http://wrap.warwick.ac.uk/id/eprint/15231

Data sourced from Thomson Reuters' Web of Knowledge

Request changes to a record

Actions (login required)

View Item