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libFLASM: a software library for fixed-length approximate string matching.

Lorraine A K Ayad1, Solon P P Pissis2, Ahmad Retha1

  • 1Department of Informatics, King's College London, The Strand, London, WC2R 2LS, UK.

BMC Bioinformatics
|November 12, 2016
PubMed
Summary

We introduce libFLASM, a C++ library for fixed-length approximate string matching, applicable to computational biology. This tool efficiently solves problems using edit and Hamming distances, showing competitive performance.

Keywords:
Approximate string matchingDynamic programmingFixed-length approximate string matchingSoftware library

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Algorithm Development

Background:

  • Approximate string matching identifies text factors within a specified distance k from a pattern.
  • Fixed-length approximate string matching extends this to factors of specific lengths (l) within a pattern of length m.
  • Existing bit-vector techniques offer efficient solutions independent of distance threshold (k) or alphabet size.

Purpose of the Study:

  • To present libFLASM, a free, open-source C++ software library for fixed-length approximate string matching.
  • To demonstrate the application of fixed-length approximate string matching in solving real-world problems.
  • To improve accuracy in multiple circular sequence alignment and motif extraction.

Main Methods:

  • Developed libFLASM, a C++ library implementing fixed-length approximate string matching.
  • Utilized edit and Hamming distance models for string matching.
  • Integrated libFLASM into applications for sequence alignment and motif extraction.

Main Results:

  • libFLASM provides efficient solutions for fixed-length approximate string matching.
  • The library improves accuracy in multiple circular sequence alignment and motif extraction.
  • Performance is competitive, particularly with increasing distance thresholds.

Conclusions:

  • Fixed-length approximate string matching is a valuable generalization of classic approximate string matching.
  • libFLASM is a robust open-source library with potential for broad application.
  • Further development of libFLASM is recommended to benefit diverse applications.