Journal article
Gene transcript clustering: a comparison of parallel approaches
Future Generation Computer Systems, Vol.21(5), pp.731-735
2005
DOI: 10.1016/j.future.2004.05.014
Abstract
One of the fundamental components of large-scale gene discovery projects is that of clustering of expressed sequence tags (ESTs) from complementary DNA (cDNA) clone libraries. Clustering is used to create non-redundant catalogs and indices of these sequences. In particular, clustering of ESTs is frequently used to estimate the number of genes derived from cDNA-based gene discovery efforts. This paper presents a novel parallel extension to an EST clustering program, UIcluster4, that incorporates alternative splicing information and a new parallelization strategy. The results are compared to other parallelized EST clustering systems in terms of overall processing time and in accuracy of the resulting clustering.
Details
- Title: Subtitle
- Gene transcript clustering: a comparison of parallel approaches
- Creators
- Todd E Scheetz - Departments of Electrical and Computer Engineering, Biomedical Engineering, and Ophthalmology and Visual Sciences, Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IW 52242, USANishank Trivedi - Departments of Electrical and Computer Engineering, Biomedical Engineering, and Ophthalmology and Visual Sciences, Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IW 52242, USAKevin T Pedretti - Sandia National Laboratories, Albuquerque, New Mexico 87123, USATerry A Braun - Departments of Electrical and Computer Engineering, Biomedical Engineering, and Ophthalmology and Visual Sciences, Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IW 52242, USAThomas L Casavant - Departments of Electrical and Computer Engineering, Biomedical Engineering, and Ophthalmology and Visual Sciences, Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IW 52242, USA
- Resource Type
- Journal article
- Publication Details
- Future Generation Computer Systems, Vol.21(5), pp.731-735
- Publisher
- Elsevier B.V
- DOI
- 10.1016/j.future.2004.05.014
- ISSN
- 0167-739X
- eISSN
- 1872-7115
- Language
- English
- Date published
- 2005
- Academic Unit
- Ophthalmology and Visual Sciences; Electrical and Computer Engineering; Roy J. Carver Department of Biomedical Engineering
- Record Identifier
- 9983979923602771
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