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Journal of Parallel and Distributed Computing
Volume 66, Issue 12, December 2006, Pages 1482-1488
Special Issue: Grids in Bioinformatics and Computational Biology
 
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doi:10.1016/j.jpdc.2006.08.009    How to Cite or Link Using DOI (Opens New Window)
Copyright © 2006 Published by Elsevier Inc.

High performance cDNA sequence analysis using grid technology

G.A. Trombettia, b, E-mail The Corresponding Author, I. Merellia, Corresponding Author Contact Information, E-mail The Corresponding Author and L. Milanesia, E-mail The Corresponding Author

aIstituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, Segrate (Milano), Italy bUniversità degli Studi di Bologna, Facoltà di Ingegneria, v.le del Risorgimento 2, Bologna, Italy

Received 10 September 2005; 
revised 22 July 2006; 
accepted 15 August 2006. 
Available online 16 October 2006.

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Abstract

Innovative DNA sequencers, relying on pyrosequencing, are now being produced, which cut down costs and speed up sequencing by an order of magnitude. Hence the capability of handling high throughput sequencing is becoming increasingly important for Bioinformatics.

This study concerns the development of a high performance pipeline for analyzing cDNA sequences produced by a high throughput pyrosequencer. Mainly, this analysis system has been developed by us to map the sequenced cDNA strands against a cDNA database for studying different mutations that can influence the genes functionality. The pipeline supports heterozygous organisms.

In order to use a high throughput pyrosequencer fruitfully, the related bioinformatics analysis requires high performance. Hence we implemented our analysis system leveraging the European EGEE project infrastructure: a network of several computational resources and storage facilities distributed at different sites.

The results of this high performance pipeline are stored into an output database directly from the grid sites using the Web Services technology. By querying this database it is possible to inspect the analysis results to detect different mutations in the cDNA sequences, as well as other meaningful biological parameters and information.

Keywords: Bioinformatics; Grid; High performance; Sequencing; cDNA; Distributed; Web services


Journal of Parallel and Distributed Computing
Volume 66, Issue 12, December 2006, Pages 1482-1488
Special Issue: Grids in Bioinformatics and Computational Biology
 
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