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An overview of the wcd EST clustering tool
Scott Hazelhurst1, Winston Hide, Zsuzsanna Lipták
1Wits Bioinformatics, University of the Witwatersrand, Johannesburg, Private Bag 3, 2050 Wits, South Africa. scott.hazelhurst@wits.ac.za
Bioinformatics (Oxford, England)
|May 16, 2008
Summary
The wcd system offers efficient clustering for expressed sequence tags (ESTs) and other nucleic acid sequences. This open-source tool enhances sequence comparison and cluster management, improving bioinformatics workflows.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Expressed sequence tags (ESTs) and other DNA/RNA sequences require efficient clustering for analysis.
- Existing clustering tools may have limitations in speed and functionality.
Purpose of the Study:
- To introduce wcd, an open-source system for clustering expressed sequence tags (ESTs) and other nucleic acid sequences.
- To provide an improved implementation of sequence comparison algorithms, specifically d(2) distance and edit distance.
Main Methods:
- The wcd system implements all-versus-all sequence comparison using d(2) and edit distance.
- It supports cluster merging, refinement, and reclustering operations.
- wcd is compatible with the StackPack clustering package and supports parallelization.
Main Results:
- wcd provides efficient all-versus-all comparison of ESTs, improving upon existing d(2) implementations.
- The system supports advanced cluster manipulation, including merging and refinement.
- Parallelization capabilities enhance performance on both shared memory and cluster architectures.
Conclusions:
- wcd is a versatile and efficient open-source tool for sequence clustering in bioinformatics.
- Its compatibility and parallelization features make it suitable for large-scale genomic data analysis.
- The EMBOSS wrapper facilitates integration into existing bioinformatics pipelines and web servers.
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