A basic analysis toolkit for biological sequences

Raffaele Giancarlo, Filippo Utro

Risultato della ricerca: Articlepeer review

4 Citazioni (Scopus)

Abstract

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at http://www.math.unipa.it/~raffaele/BATS/
Lingua originaleEnglish
Numero di pagine16
RivistaAlgorithms for Molecular Biology
Volume2007
Stato di pubblicazionePublished - 2007

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics

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