ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes

Otto, T. D. et al. (2010) ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics, 26(5), pp. 705-707. (doi: 10.1093/bioinformatics/btq011) (PMID:20089515) (PMCID:PMC2828119)

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Abstract

Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Otto, T. D., Catanho, M., Tristao, C., Bezerra, M., Fernandes, R. M., Elias, G. S., Scaglia, A. C., Bovermann, B., Berstis, V., Lifschitz, S., de Miranda, A. B., and Degrave, W.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Copyright Holders:Copyright ©2010 The Authors
First Published:First published in Bioinformatics 26(5):705-707
Publisher Policy:Reproduced under a Creative Commons License

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