title: GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags.
abstract: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.
authors.affiliation: Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universitàe Ricerca, CASPUR, Rome, Italy.
authors.forename: Tiziana
authors.initials: T
authors.lastname: Castrignanò
authors.forename: Paolo D'Onorio
authors.initials: PD
authors.lastname: De Meo
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: Ivano Giuseppe
authors.initials: IG
authors.lastname: Talamo
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D017124:Conserved Sequence; D020224:Expressed Sequence Tags; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface