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

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 p...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella, Carlo Pozzi
• Keywords: BMCBI 2008, Database, ESTree Db, Sequences