title: ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The database can be accessed through http://proteinworlddb.org
authors.affiliation: Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil. otto@fiocruz.br
authors.forename: Thomas Dan
authors.initials: TD
authors.lastname: Otto
authors.forename: Marcos
authors.initials: M
authors.lastname: Catanho
authors.forename: Cristian
authors.initials: C
authors.lastname: Tristão
authors.forename: Márcia
authors.initials: M
authors.lastname: Bezerra
authors.forename: Renan Mathias
authors.initials: RM
authors.lastname: Fernandes
authors.forename: Guilherme Steinberger
authors.initials: GS
authors.lastname: Elias
authors.forename: Alexandre Capeletto
authors.initials: AC
authors.lastname: Scaglia
authors.forename: Bill
authors.initials: B
authors.lastname: Bovermann
authors.forename: Viktors
authors.initials: V
authors.lastname: Berstis
authors.forename: Sergio
authors.initials: S
authors.lastname: Lifschitz
authors.forename: Antonio Basílio
authors.initials: AB
authors.lastname: de Miranda
authors.forename: Wim
authors.initials: W
authors.lastname: Degrave
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016678:Genome; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins