title: A user-friendly web portal for T-Coffee on supercomputers.
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.
authors.affiliation: Department of Computer Science and Industrial Engineering, University of Lleida, C/Jaume II 69, E-25001 Lleida, Spain. jrius@diei.udl.cat
authors.forename: Josep
authors.initials: J
authors.lastname: Rius
authors.forename: Fernando
authors.initials: F
authors.lastname: Cores
authors.forename: Francesc
authors.initials: F
authors.lastname: Solsona
authors.forename: Jano I
authors.initials: JI
authors.lastname: van Hemert
authors.forename: Jos
authors.initials: J
authors.lastname: Koetsier
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D016000:Cluster Analysis; D023281:Genomics / Q000379:methods*; D020407:Internet; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins