Skip Navigation



Bioinformatics Advance Access published online on November 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti754
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/4/497    most recent
bti754v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Castrignanò, T.
Right arrow Articles by Pesole, G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Castrignanò, T.
Right arrow Articles by Pesole, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 27, 2005
Revised September 14, 2005
Accepted October 28, 2005

Applications note

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 4*

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


  Abstract

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: (i) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (ii) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes; (iii) 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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.