title: PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.
abstract: 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.
authors.affiliation: Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8. paullu@cs.ualberta.ca
authors.forename: Paul
authors.initials: P
authors.lastname: Lu
authors.forename: Duane
authors.initials: D
authors.lastname: Szafron
authors.forename: Russell
authors.initials: R
authors.lastname: Greiner
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
authors.forename: Alona
authors.initials: A
authors.lastname: Fyshe
authors.forename: Brandon
authors.initials: B
authors.lastname: Pearcy
authors.forename: Brett
authors.initials: B
authors.lastname: Poulin
authors.forename: Roman
authors.initials: R
authors.lastname: Eisner
authors.forename: Danny
authors.initials: D
authors.lastname: Ngo
authors.forename: Nicholas
authors.initials: N
authors.lastname: Lamb
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001185:Artificial Intelligence; D030562:Databases, Protein; D006801:Humans; D051379:Mice; D023421:Models, Animal; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D040901:Proteomics; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins