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DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences (1999)
| Venue: | J Mol Biol |
| Citations: | 214 - 10 self |
BibTeX
@ARTICLE{Jones99dt:genthreader:,
author = {David T. Jones},
title = {DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences},
journal = {J Mol Biol},
year = {1999}
}
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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 ®nal step, each threaded model is evaluated by a neural network in order to produce a single measure of con®dence 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 signi®cant 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. # 1999 Academic Press
Keyphrases
reliable protein fold recognition method genomic sequence con dence nal step mycoplasma genitalium traditional sequence alignment algorithm translated bacterial genome total coverage low false-positive rate known structure amino acid residue threaded model signi cant relationship single measure new protein fold recognition method whole proteome neural network academic press
