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

Area of Science:

• Plant genomics
• Bioinformatics
• Molecular biology

Background:

• The ESTree database aggregates expressed sequence tag (EST) data for Prunus persica (peach) and Prunus dulcis (almond).
• Version VI incorporates 75,404 sequences from 19 peach and 3 almond libraries, representing diverse genotypes, tissues, and fruit developmental stages.

Purpose of the Study:

• To enhance the existing ESTree database with new sequences and advanced analysis programs.
• To improve the web interface for more intuitive and comprehensive querying of database features.

Main Methods:

• A modular Perl pipeline was developed for sequence analysis, with outputs automatically stored in a MySQL database.
• New tools were implemented for tandem repeat identification, annotation against Rosaceae genomes, and integration of microarray data.
• Protein pattern identification using PROSITE and GO functional category analysis were performed.

Main Results:

• The updated ESTree db (version VI) includes advanced analyses such as tandem repeat identification and genomic annotation.
• New functionalities allow tracking of homologous hits on the Gene Ontology (GO) tree and statistical analysis of ontologies.
• The PHP-based web interface was upgraded for multi-faceted querying based on biological features.

Conclusions:

• Version VI of the ESTree db provides a comprehensive resource for peach gene expression analysis.
• Linked to external resources, the database offers extensive, queryable information via its web interface.
• The flexible and modular design facilitates adaptation for similar datasets with minimal manual effort.