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

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2011
Author
Rius Torrentó, Josep Maria
Cores Prado, Fernando
Solsona Tehàs, Francesc
Hemert, Jano van
Koetsier, Jos
Notredame, Cedric
Suggested citation
Rius Torrentó, Josep Maria; Cores Prado, Fernando; Solsona Tehàs, Francesc; Hemert, Jano van; Koetsier, Jos; Notredame, Cedric; . (2011) . A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinformatics, 2011, vol. 12, núm. 150, p. 1-5. https://doi.org/10.1186/1471-2105-12-150.
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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.
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http://hdl.handle.net/10459.1/41533
DOI
https://doi.org/10.1186/1471-2105-12-150
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BMC Bioinformatics, 2011, vol. 12, núm. 150, p. 1-5
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cc-by, (c) Rius et al., 2011
Except where otherwise noted, this item's license is described as cc-by, (c) Rius et al., 2011