ARS | Publication request: EST-PAGE: A TOOL FOR MANAGING AND ANALYZING EST DATA

Submitted to: International Genome Sequencing and Analysis Conference
Publication Type: Abstract
Publication Acceptance Date: August 31, 2003
Publication Date: September 1, 2003
Citation: Matukumalli, L.K., Grefenstette, J.J., Sonstegard, T.S., Van Tassell, C.P. 2003. Est-page: a tool for managing and analyzing EST data [abstract]. TIGR XV GSAC Conference, September 2003.

Technical Abstract: EST-PAGE is an application that integrates disparate tools to answer complex biological questions with EST (expressed sequence tags) data. PAGE is an acronym summarizing the applications features: P (Processing of chromatograms including base calling), A (Analysis of the sequence data with vector masking, low complexity filtering, and E.coli contamination screening), G (GenBank dbEST submission), E (Exploration of EST data by clustering and annotation). EST-PAGE addresses experimental quality control issues (library construction, plate maintenance, sequencing protocol, and instrument performance) for optimal use of resources in sequencing projects. Extensive data analysis and visualization tools are included to maximize impact of the data. The source code of EST-PAGE is made available for free by contacting the authors. EST-PAGE is written in Perl, and takes advantage of standard modules such as bioperl and CGI-Perl. Open source databases Postgres or MySql can be used to store the data. EST-PAGE is user friendly, can be easily installed and generalized so that it used by diverse groups working on plant or animal species as a common resource. Automated BLAST matches, Gene Ontology annotations and SNP detection algorithms are being added to extend the functionality of this application. A demonstration site is located at http://est-page.binf.gmu.edu.