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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2007

Open Access Research

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

Barbara Lazzari1*, Andrea Caprera1, Alberto Vecchietti1, Ivan Merelli2, Francesca Barale3, Luciano Milanesi2, Alessandra Stella1 and Carlo Pozzi1

Author Affiliations

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

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

3 Università degli Studi di Milano, Facoltà di Scienze Agrarie, via Celoria 2, Milan, 20133, Italy

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BMC Bioinformatics 2008, 9(Suppl 2):S9  doi:10.1186/1471-2105-9-S2-S9

Published: 26 March 2008

Abstract

Background

The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features.

Results

A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features.

Conclusions

The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention.