Journal
BIOINFORMATICS
Volume 19, Issue 18, Pages 2498-2499Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btg360
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SPEPlip is a neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes. SPEPlip identifies the presence of sorting signals and predicts their cleavage sites. The accuracy in cross-validation is similar to that of other available programs: the rate of false positives is 4 and 6%, for prokaryotes and eukaryotes respectively and that of false negatives is 3% in both cases. When a set of 409 prokaryotic lipoproteins is predicted, SPEPlip predicts 97% of the chains in the signal peptide class. However, by integrating SPEPlip with a regular expression search utility based on the PROSITE pattern, we can successfully discriminate signal peptide-containing chains from lipoproteins. We propose the method for detecting and discriminating signal peptides containing chains and lipoproteins.
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