Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

Paolo Di Tommaso; Miquel Orobitg; Fernando Guirado; Fernado Cores; Toni Espinosa; Cedric Notredame

doi:10.1093/bioinformatics/btq304

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

Bioinformatics. 2010 Aug 1;26(15):1903-4. doi: 10.1093/bioinformatics/btq304. Epub 2010 Jul 6.

Authors

Paolo Di Tommaso¹, Miquel Orobitg, Fernando Guirado, Fernado Cores, Toni Espinosa, Cedric Notredame

Affiliation

¹ Centre For Genomic Regulation (Pompeu Fabra University), Carrer del Doctor Aiguader 88, Barcelona, Spain.

Abstract

Summary: We present the first parallel implementation of the T-Coffee consistency-based multiple aligner. We benchmark it on the Amazon Elastic Cloud (EC2) and show that the parallelization procedure is reasonably effective. We also conclude that for a web server with moderate usage (10K hits/month) the cloud provides a cost-effective alternative to in-house deployment.

Availability: T-Coffee is a freeware open source package available from http://www.tcoffee.org/homepage.html

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Internet
Sequence Alignment / methods*
Software*