A user-friendly web portal for T-Coffee on supercomputers
Hemert, Jano van
MetadataShow full item record
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.
Is part ofBMC Bioinformatics, 2011, vol. 12, núm. 150, p. 1-5
European research projects
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
Lladós Segura, Jordi; Guirado Fernández, Fernando; Cores Prado, Fernando; Lérida Monsó, Josep Lluís; Notredame, Cedric (Springer Verlag, 2015-05-01)Multiple sequence alignment (MSA) is crucial for high-throughput next generation sequencing applications. Large-scale alignments with thousands of sequences are necessary for these applications. However, the quality of the ...
High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Cores Prado, Fernando; Lladós Segura, Jordi; Notredame, Cedric (Elsevier, 2014-10-08)Multiple Sequence Alignment (MSA) is essential for a wide range of applications in Bioinformatics. Traditionally, the alignment accuracy was the main metric used to evaluate the goodness of MSA tools. However, with the ...
Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Notredame, Cedric; Cores Prado, Fernando (Springer Verlag, 2011)Multiple Sequence Alignment (MSA) constitutes an extremely powerful tool for important biological applications such as phylogenetic analysis, identification of conserved motifs and domains and structure prediction. In ...