GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences 1 1 Edited by B. Honig

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences 1 1... A new protein fold recognition method is described which is both fast and reliable. The method uses a traditional sequence alignment algorithm to generate alignments which are then evaluated by a method derived from threading techniques. As a final step, each threaded model is evaluated by a neural network in order to produce a single measure of confidence in the proposed prediction. The speed of the method, along with its sensitivity and very low false-positive rate makes it ideal for automatically predicting the structure of all the proteins in a translated bacterial genome (proteome). The method has been applied to the genome of Mycoplasma genitalium , and analysis of the results shows that as many as 46 % of the proteins derived from the predicted protein coding regions have a significant relationship to a protein of known structure. In some cases, however, only one domain of the protein can be predicted, giving a total coverage of 30 % when calculated as a fraction of the number of amino acid residues in the whole proteome. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Molecular Biology Elsevier

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences 1 1 Edited by B. Honig

Journal of Molecular Biology, Volume 287 (4) – Apr 9, 1999

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Publisher
Elsevier
Copyright
Copyright © 1999 Academic Press
ISSN
0022-2836
DOI
10.1006/jmbi.1999.2583
pmid
10191147
Publisher site
See Article on Publisher Site

Abstract

A new protein fold recognition method is described which is both fast and reliable. The method uses a traditional sequence alignment algorithm to generate alignments which are then evaluated by a method derived from threading techniques. As a final step, each threaded model is evaluated by a neural network in order to produce a single measure of confidence in the proposed prediction. The speed of the method, along with its sensitivity and very low false-positive rate makes it ideal for automatically predicting the structure of all the proteins in a translated bacterial genome (proteome). The method has been applied to the genome of Mycoplasma genitalium , and analysis of the results shows that as many as 46 % of the proteins derived from the predicted protein coding regions have a significant relationship to a protein of known structure. In some cases, however, only one domain of the protein can be predicted, giving a total coverage of 30 % when calculated as a fraction of the number of amino acid residues in the whole proteome.

Journal

Journal of Molecular BiologyElsevier

Published: Apr 9, 1999

References

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