GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags

• Published in: Bioinformatics Vol. 22; no. 4; pp. 497 - 499
• Main Authors: Castrignanò, Tiziana, De Meo, Paolo D'Onorio, Grillo, Giorgio, Liuni, Sabino, Mignone, Flavio, Talamo, Ivano Giuseppe, Pesole, Graziano
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.02.2006; Oxford Publishing Limited (England)
• Subjects: Algorithms; Base Sequence; Biological and medical sciences; Chromosome Mapping - methods; Computer Graphics; Conserved Sequence; Expressed Sequence Tags; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Open Reading Frames; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Sequence Homology, Nucleic Acid; Software; User-Computer Interface; Alignment; Conserved sequence; Graphical interface; Non coding sequence; Homology; Joining; Software; Genome; Web site; Bioinformatics; Sequence tagged site; Scope note
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti754

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. Availability: . GenoMiner software and documentation is available from the authors upon request. Contact: graziano.pesole@unimi.it