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Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
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A user-friendly web portal for T-Coffee on supercomputers.

Josep Rius1, Fernando Cores, Francesc Solsona

  • 1Department of Computer Science and Industrial Engineering, University of Lleida, C/Jaume II 69, E-25001 Lleida, Spain. jrius@diei.udl.cat

BMC Bioinformatics
|May 17, 2011
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Summary
This summary is machine-generated.

A new web portal makes Parallel T-Coffee (PTC), a tool for large-scale sequence alignment, accessible to users without supercomputing experience. This enhances usability for complex bioinformatics tasks.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Parallel T-Coffee (PTC) is a parallel implementation of the T-Coffee multiple sequence alignment tool designed to reduce execution time for large-scale alignments.
  • PTC utilizes MPI and RMA mechanisms and can run on distributed memory clusters, enabling alignment of hundreds of proteins.
  • A significant barrier to PTC adoption is the lack of familiarity among potential users with grids or supercomputers.

Purpose of the Study:

  • To demonstrate the easy deployment and control of Parallel T-Coffee on supercomputer architectures.
  • To provide a user-friendly solution for accessing advanced computational resources for sequence alignment.

Main Methods:

  • Development of a web portal using the Rapid tool for application standardization and deployment.
  • Integration of Parallel T-Coffee into a web portal for simplified user interaction.
  • The approach is designed to be generic for deployment on various High-Performance Computing (HPC) environments.

Main Results:

  • Parallel T-Coffee can be effectively deployed and controlled on supercomputer architectures via a web portal.
  • The Rapid tool facilitated the creation of standardized portlets for application deployment.
  • The developed approach is adaptable for deploying PTC on different HPC environments.

Conclusions:

  • The PTC web portal enables users to align large sequence datasets that are unmanageable on single machines due to memory and time constraints.
  • The web portal offers an accessible and user-friendly interface for advanced sequence alignment capabilities.
  • This solution lowers the barrier to entry for utilizing powerful parallel computing resources in bioinformatics.