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[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

Ying Xu1, Yi-xue Li, Xiang-yin Kong

  • 1Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, China.

Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
|July 26, 2005
PubMed
Summary
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GNU Pattern (Gpat) is a new open-source software engine that efficiently implements the SPLASH algorithm for pattern discovery. Its open availability facilitates further research in biological sequence pattern recognition.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Context:

  • Developing high-performance software is crucial for advancing pattern discovery in biological sequences.
  • The SPLASH algorithm offers a robust framework for sequence analysis.
  • Open-source software promotes collaboration and reproducibility in research.

Purpose:

  • To construct a high-performance, open-source software engine based on the IBM SPLASH algorithm.
  • To facilitate future research in pattern discovery within biological sequences.
  • To provide a modifiable software framework for the scientific community.

Summary:

  • GNU Pattern (Gpat) software has been developed, efficiently implementing the core components of the SPLASH algorithm.
  • Gpat is built using open-source software principles.

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  • The complete source code is released under the GNU license, enabling modification and extension by other researchers.

    • Impact:

    • Gpat represents a successful implementation of the SPLASH algorithm.
    • The software serves as a foundational framework for subsequent pattern recognition research in biological sequences.
    • The open-source nature of Gpat encourages broader adoption and advancement in the field.