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Open Access Highly Accessed Software

A user-friendly web portal for T-Coffee on supercomputers

Josep Rius1*, Fernando Cores1, Francesc Solsona1, Jano I van Hemert2, Jos Koetsier2 and Cedric Notredame3

Author Affiliations

1 Department of Computer Science and Industrial Engineering, University of Lleida, C/Jaume II 69, E-25001 Lleida, Spain

2 UK National e-Science Centre, University of Edinburgh, 10 Crichton Street, EH8 9AB, Edinburgh, UK

3 Centre For Genomic Regulation (Pompeu Fabra University), C/Doctor Aiguader 88, 08003 Barcelona, Spain

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BMC Bioinformatics 2011, 12:150  doi:10.1186/1471-2105-12-150

Published: 12 May 2011

Abstract

Background

Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers.

Results

In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments.

Conclusions

The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.