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Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.

Goldman, N; Thorne, JL; Jones, DT; (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol , 263 (2) pp. 196-208. 10.1006/jmbi.1996.0569.

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Abstract

Previously proposed methods for protein secondary structure prediction from multiple sequence alignments do not efficiently extract the evolutionary information that these alignments contain. The predictions of these methods are less accurate than they could be, because of their failure to consider explicitly the phylogenetic tree that relates aligned protein sequences. As an alternative, we present a hidden Markov model approach to secondary structure prediction that more fully uses the evolutionary information contained in protein sequence alignments. A representative example is presented, and three experiments are performed that illustrate how the appropriate representation of evolutionary relatedness can improve inferences. We explain why similar improvement can be expected in other secondary structure prediction methods and indeed any comparative sequence analysis method.

Type: Article
Title: Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.
Location: ENGLAND
DOI: 10.1006/jmbi.1996.0569
Keywords: Amino Acid Sequence, Evolution, Molecular, Models, Theoretical, Molecular Sequence Data, Protein Structure, Secondary, Proteins, Sequence Analysis
UCL classification: UCL > School of BEAMS
UCL > School of BEAMS > Faculty of Engineering Science
URI: http://discovery.ucl.ac.uk/id/eprint/103230
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