Nucleic Acids Research, 2005, Vol. 33, Database issue D147-D153
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
* To whom correspondence should be addressed. Tel: +1 780 492 7760; Fax: +1 780 492 1071; Email: paullu{at}cs.ualberta.ca
Received August 15, 2004; Revised and Accepted October 20, 2004
PA-GOSUB (Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization) is a publicly available, web-based, searchable and downloadable database that contains the sequences, predicted GO molecular functions and predicted subcellular localizations of more than 107 000 proteins from 10 model organisms (and growing), covering the major kingdoms and phyla for which annotated proteomes exist (http://www.cs.ualberta.ca/~bioinfo/PA/GOSUB). The PA-GOSUB database effectively expands the coverage of subcellular localization and GO function annotations by a significant factor (already over five for subcellular localization, compared with Swiss-Prot v42.7), and more model organisms are being added to PA-GOSUB as their sequenced proteomes become available. PA-GOSUB can be used in three main ways. First, a researcher can browse the pre-computed PA-GOSUB annotations on a per-organism and per-protein basis using annotation-based and text-based filters. Second, a user can perform BLAST searches against the PA-GOSUB database and use the annotations from the homologs as simple predictors for the new sequences. Third, the whole of PA-GOSUB can be downloaded in either FASTA or comma-separated values (CSV) formats.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. Casadio, P. L. Martelli, and A. Pierleoni The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation Brief Funct Genomic Proteomic, February 18, 2008; (2008) eln003v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. S. Srinivasan, N. H. Shah, J. A. Flannick, E. Abeliuk, A. F. Novak, and S. Batzoglou Current progress in network research: toward reference networks for key model organisms Brief Bioinform, September 1, 2007; 8(5): 318 - 332. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Pierleoni, P. L. Martelli, P. Fariselli, and R. Casadio eSLDB: eukaryotic subcellular localization database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D208 - D212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Friedberg Automated protein function prediction--the genomic challenge Brief Bioinform, September 1, 2006; 7(3): 225 - 242. [Abstract] [Full Text] [PDF]
|
|