An overview of the wcd EST clustering tool

Hazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R (2008)
BIOINFORMATICS 24(13): 1542-1546.

Journal Article | Published | English

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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).
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Hazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R. An overview of the wcd EST clustering tool. BIOINFORMATICS. 2008;24(13):1542-1546.
Hazelhurst, S., Hide, W., Lipták, Z., Nogueira, R., & Starfield, R. (2008). An overview of the wcd EST clustering tool. BIOINFORMATICS, 24(13), 1542-1546.
Hazelhurst, S., Hide, W., Lipták, Z., Nogueira, R., and Starfield, R. (2008). An overview of the wcd EST clustering tool. BIOINFORMATICS 24, 1542-1546.
Hazelhurst, S., et al., 2008. An overview of the wcd EST clustering tool. BIOINFORMATICS, 24(13), p 1542-1546.
S. Hazelhurst, et al., “An overview of the wcd EST clustering tool”, BIOINFORMATICS, vol. 24, 2008, pp. 1542-1546.
Hazelhurst, S., Hide, W., Lipták, Z., Nogueira, R., Starfield, R.: An overview of the wcd EST clustering tool. BIOINFORMATICS. 24, 1542-1546 (2008).
Hazelhurst, Scott, Hide, Winston, Lipták, Zsuzsanna, Nogueira, Ramon, and Starfield, Richard. “An overview of the wcd EST clustering tool”. BIOINFORMATICS 24.13 (2008): 1542-1546.
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Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development.
Passos MA, de Cruz VO, Emediato FL, de Teixeira CC, Azevedo VC, Brasileiro AC, Amorim EP, Ferreira CF, Martins NF, Togawa RC, Junior GJ, da Silva OB Jr, Miller RN., BMC Genomics 14(), 2013
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Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates.
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KABOOM! A new suffix array based algorithm for clustering expression data.
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SEED: efficient clustering of next-generation sequences.
Bao E, Jiang T, Kaloshian I, Girke T., Bioinformatics 27(18), 2011
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Revealing impaired pathways in the an11 mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes.
Zenoni S, D'Agostino N, Tornielli GB, Quattrocchio F, Chiusano ML, Koes R, Zethof J, Guzzo F, Delledonne M, Frusciante L, Gerats T, Pezzotti M., Plant J. 68(1), 2011
PMID: 21623977
High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species.
Grattapaglia D, Silva-Junior OB, Kirst M, de Lima BM, Faria DA, Pappas GJ Jr., BMC Plant Biol. 11(), 2011
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Clustering algorithms in biomedical research: a review.
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PEACE: Parallel Environment for Assembly and Clustering of Gene Expression.
Rao DM, Moler JC, Ozden M, Zhang Y, Liang C, Karro JE., Nucleic Acids Res. 38(Web Server issue), 2010
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SolEST database: a "one-stop shop" approach to the study of Solanaceae transcriptomes.
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EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.
Picardi E, Mignone F, Pesole G., BMC Bioinformatics 10 Suppl 6(), 2009
PMID: 19534735

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