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Bioinformatics. 2008 Jul 1;24(13):1542-6. doi: 10.1093/bioinformatics/btn203. Epub 2008 May 14.

An overview of the wcd EST clustering tool.

Author information

  • 1Wits Bioinformatics, University of the Witwatersrand, Johannesburg, Private Bag 3, 2050 Wits, South Africa. scott.hazelhurst@wits.ac.za

Abstract

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.

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.

PMID:
18480101
[PubMed - indexed for MEDLINE]
PMCID:
PMC2718666
Free PMC Article

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