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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2005

Open Access Research article

ESTree db: a Tool for Peach Functional Genomics

Barbara Lazzari1*, Andrea Caprera2, Alberto Vecchietti1, Alessandra Stella1, Luciano Milanesi3 and Carlo Pozzi1

Author Affiliations

1 Parco Tecnologico Padano, Via Einstein – Località Cascina Codazza, 26900 Lodi, Italy

2 CISI, Via Fratelli Cervi 93, 20090 Segrate (MI), Italy

3 Istituto Tecnologie Biomediche, Via Fratelli Cervi 93, 20090 Segrate (MI), Italy

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BMC Bioinformatics 2005, 6(Suppl 4):S16  doi:10.1186/1471-2105-6-S4-S16

Published: 1 December 2005

Abstract

Background

The ESTree db http://www.itb.cnr.it/estree/ webcite represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database.

Results

The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories.

Conclusion

The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.