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Bioinformatics Advance Access originally published online on November 2, 2005
Bioinformatics 2006 22(4):497-499; doi:10.1093/bioinformatics/bti754
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Tiziana Castrignanò 1, Paolo D'Onorio De Meo 1, Giorgio Grillo 2, Sabino Liuni 2, Flavio Mignone 3, Ivano Giuseppe Talamo 1 and Graziano Pesole 2,3,*

1Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universitàe Ricerca, CASPUR Rome, Italy
2Istituto Tecnologie Biomediche, Sede di Bari Consiglio Nazionale delle Ricerche, Italy
3University of Milan, Dipartimento di Scienze Biomolecolari e Biotecnologie via Celoria 26, Milan 20133, Italy

*To whom correspondence should be addressed.

Summary: 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: http://www.caspur.it/GenoMiner/. GenoMiner software and documentation is available from the authors upon request.

Contact: graziano.pesole{at}unimi.it

Received on June 27, 2005; revised on September 14, 2005; accepted on October 28, 2005

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