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Bioinformatics Advance Access published online on May 14, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn203
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© 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.

An overview of the wcd EST Clustering Tool

Scott Hazelhurst a,*, Winston Hide b, Zsuzsanna Lipták c, Ramon Nogueira a and Richard Starfield a

aWits Bioinformatics, University of the Witwatersrand, Johannesburg, Private Bag 3, 2050 Wits, South Africa; bSouth African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; cUniversität Bielefeld, AG Genominformatik, Technische Fakultät, Postfach 100131, 33501Bielefeld, Germany

*To whom correspondence should be addressed. Dr. Scott Hazelhurst, E-mail: scott.hazelhurst{at}wits.ac.za


  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 parallelisation under both SMP 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{at}wits.ac.za

Supplementary information: Additional experimental results. The wcd manual, a companion paper describing underlying algorithms, and all data sets used for experimentation can also be found at www.bioinf.wits.ac.za/~scott/wcdsupp.html

Associate Editor: Prof. David Rocke

Received on October 30, 2007; revised on March 21, 2008; accepted on April 20, 2008

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