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Bioinformatics Advance Access originally published online on May 14, 2008
Bioinformatics 2008 24(13):1542-1546; 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 1,*, Winston Hide 2, Zsuzsanna Lipták 3, Ramon Nogueira 1 and Richard Starfield 1

1Wits Bioinformatics, University of the Witwatersrand, Johannesburg, Private Bag 3, 2050 Wits, 2South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa and 3Universität Bielefeld, AG Genominformatik, Technische Fakultät, Postfach 100131, 33501 Bielefeld, Germany

*To whom correspondence should be addressed.


  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 d 2 distance function or edit distance, improving existing implementations of d 2. 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{at}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

Associate Editor: David Rocke

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

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