title: CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison.
abstract: The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features.
authors.affiliation: Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, CASPUR, Rome, Italy.
authors.forename: Tiziana
authors.initials: T
authors.lastname: Castrignanò
authors.forename: Alessandro
authors.initials: A
authors.lastname: Canali
authors.forename: Giorgio
authors.initials: G
authors.lastname: Grillo
authors.forename: Sabino
authors.initials: S
authors.lastname: Liuni
authors.forename: Flavio
authors.initials: F
authors.lastname: Mignone
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D000818:Animals; D003196:Computer Graphics; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000032:analysis*; D005091:Exons; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D012045:Regulatory Sequences, Nucleic Acid; D016324:Sequence Tagged Sites; D012984:Software; D014584:User-Computer Interface
chemical_list: D021901:DNA, Intergenic