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SeqAn an efficient, generic C++ library for sequence analysis.

Andreas Döring1, David Weese, Tobias Rausch

  • 1Algorithmische Bioinformatik, Institut für Informatik, Takustr, 9, 14195 Berlin, Germany. doering@inf.fu-berlin.de

BMC Bioinformatics
|January 11, 2008
PubMed
Summary
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SeqAn is a new bioinformatics library that bridges the gap between advanced algorithms and practical tools. It offers efficient components for sequence analysis, simplifying the development and comparison of bioinformatics software.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Novel algorithmic techniques are crucial for life science, yet a gap exists between advanced methods and widely used bioinformatics tools.
  • Rapid technological progress necessitates updated bioinformatics solutions.

Purpose of the Study:

  • To introduce SeqAn, a library of efficient data types and algorithms for sequence analysis.
  • To provide a foundation for testing and developing state-of-the-art bioinformatics algorithms.

Main Methods:

  • Developed SeqAn, a C++ library for computational biology.
  • Implemented practical, state-of-the-art algorithmic components for sequence analysis.
  • Demonstrated SeqAn's utility through examples: string matching algorithm comparison and a MUMmer tool variant.

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Main Results:

  • SeqAn provides efficient and versatile implementations of bioinformatics algorithms.
  • The library facilitates algorithm testing and development.
  • SeqAn enables rapid creation of new bioinformatics tools.

Conclusions:

  • SeqAn simplifies the development of new bioinformatics tools by offering readily usable algorithmic components.
  • The library supports the implementation and comparative analysis of algorithms in sequence analysis.