Hazelhurst, S., Hide, W. orcid.org/0000-0002-8621-3271, Lipták, Z. et al. (2 more authors) (2008) An overview of the wcd EST clustering tool. Bioinformatics, 24 (13). pp. 1542-1546. ISSN 1367-4803
Abstract
Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d2 distance function or edit distance, improving existing implementations of d2. It supports merging, refinement and reclustering of clusters. It is ‘drop in’ compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server). Availability: wcd is distributed under a GPL licence and is available from http://code.google.com/p/wcdest Contact: scott.hazelhurst@wits.ac.za Supplementary information: Additional experimental results. The wcd manual, a companion paper describing underlying algorithms, and all datasets used for experimentation can also be found at www.bioinf.wits.ac.za/∼scott/wcdsupp.html
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > Department of Neuroscience (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 14 Apr 2016 11:48 |
Last Modified: | 14 Apr 2016 11:48 |
Published Version: | http://dx.doi.org/10.1093/bioinformatics/btn203 |
Status: | Published |
Publisher: | Oxford University Press |
Refereed: | Yes |
Identification Number: | 10.1093/bioinformatics/btn203 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:97930 |