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Nucleic Acids Research 2004 32(Web Server Issue):W624-W627; doi:10.1093/nar/gkh486
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

Tiziana Castrignanò, Alessandro Canali, Giorgio Grillo1, Sabino Liuni1, Flavio Mignone2 and Graziano Pesole2,*

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

* To whom correspondence should be addressed. Tel: +39 02 50314915; Fax: +39 02 50314912; Email: graziano.pesole{at}unimi.it

Received February 14, 2004; Revised April 15, 2004; Accepted May 5, 2004

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.

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