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

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...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Josep Rius Torrento, Fernando Cores, Francesc Solsona, Jano I. van Hemert, Jos Koetsier, Cédric Notredame
• Keywords: Biological Datasets, Biometrics, BMCBI 2011, Multiple Sequence Alignment, Sequence Alignment Tool