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Bioinformatics Advance Access originally published online on March 24, 2007
Bioinformatics 2007 23(8):1043-1045; doi:10.1093/bioinformatics/btm063
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

GoSh: a web-based database for goat and sheep EST sequences

Andrea Caprera 1,*, Barbara Lazzari 1, Alessandra Stella 1, Ivan Merelli 2, Alexandre R. Caetano 3 and Paola Mariani 1

1Parco Tecnologico Padano, Via Einstein – Località Cascina Codazza, 26900 Lodi, 2Istituto Tecnologie Biomediche, Via Fratelli Cervi 93, 20090 Segrate (MI), Italy and 3Embrapa Recursos Geneticos e Biotecnologia Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, C.P. 02372 70770-900, Brasil

*To whom correspondence should be addressed.


  Abstract

Summary: The GoSh database is a collection of 58 990 Capra hircus and Ovis aries expressed sequence tags. A perl pipeline was prepared to process sequences, and data were collected in a MySQL database. A PHP-based web interface allows browsing and querying the database. Putative single nucleotide polymorphism (SNP) detection, as well as search to repeats were performed, and links to external related resources were provided. Sequences were annotated against three different databases and an algorithm was implemented to create statistics of the distribution of retrieved homologous ontologies in the Gene Ontology categories. The GoSh database is a repository of data and links related to goat and sheep expressed genes.

Availability: The GoSh database is available at http://www.itb.cnr.it/gosh/

Contact: andrea.caprera{at}tecnoparco.org

Associate Editor: Alfonso Valencia

Received on October 25, 2006; revised on February 5, 2007; accepted on February 16, 2007

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