Book chapter
A Parallel Expressed Sequence Tag (EST) Clustering Program
Parallel Computing Technologies, pp.490-497
Lecture Notes in Computer Science, Springer Berlin Heidelberg
08/24/2001
DOI: 10.1007/3-540-44743-1_51
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. If a naýve approach such as an NxN comparison (N is the number of sequences input) is taken, the problem is only feasible for very small data sets. UIcluster has been developed over the course of four 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 (message passing interface) standard. Both the computation and memory requirements of the program can be distributed among multiple (possibly distributed) UNIX processes.
Details
- Title: Subtitle
- A Parallel Expressed Sequence Tag (EST) Clustering Program
- Creators
- Kevin Pedretti - University of IowaTodd Scheetz - University of IowaTerry Braun - University of IowaChad Roberts - University of IowaNatalie Robinson - University of IowaThomas Casavant - University of Iowa
- Resource Type
- Book chapter
- Publication Details
- Parallel Computing Technologies, pp.490-497
- Publisher
- Springer Berlin Heidelberg; Berlin, Heidelberg
- Series
- Lecture Notes in Computer Science
- DOI
- 10.1007/3-540-44743-1_51
- eISSN
- 1611-3349
- ISSN
- 0302-9743
- Language
- English
- Date published
- 08/24/2001
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Ophthalmology and Visual Sciences; Electrical and Computer Engineering
- Record Identifier
- 9984196981302771
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