Parallel creation of non-redundant gene indices from partial mRNA Transcripts

  • Authors:

  • Nishank Trivedi;Jared Bischof;Steve Davis;Kevin Pedretti;Todd E. Scheetz;Terry A. Braun;Chad A. Roberts;Natalie L. Robinson;Val C. Sheffield;M. Bento Soares;Thomas L. Casavant

  • Affiliations:

  • Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA;Parallel Processing Laboratory, and The Coordinated Laboratory for Computational Genomics, Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA

  • Venue:
  • Future Generation Computer Systems - Parallel computing technologies (PaCT-2001)
  • Year:
  • 2002

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Abstract

This paper describes the UIcluster software tool, which partitions expressed sequence tag (EST) sequences and other genetic sequences into "clusters" based on sequence similarity. Ideally, each cluster will contain sequences that all represent the same gene. UIcluster has been developed over the course of 4 years to solve this problem efficiently and accurately for large data sets consisting of tens or hundreds of thousands of EST sequences. The latest version of the application has been parallelized using the MPI standard. Both the computation and memory requirements of the program can be distributed among multiple (possibly distributed) UNIX processes.