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BATS (Basic Analysis Toolkit for biological Sequences) is a software tool and library for the analysis of local sequence alignments by string matching, global sequence alignments by longest common subsequence (LCS) using affine or concave gap cost functions. BATS can also filter strings from sequences and compute the statistical significance as z-score and generate models.


Sequence analysis; Database management; DNA


  • Operation: Sequence analysis
  • Software interface: Command-line interface, Graphical user interface, Library
  • Language: Perl;C;C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL
  • Cost: Free
  • Version name: -
  • Credit: Italian MIUR FIRB project " Bioinformatica per la Genomica e la Proteomica", MIUR FIRB Italy-Israel project " Pattern Matching and Discovery in Discrete Structures, with applications to Bioinformatics".
  • Contact: raffaele _at_
  • Collection: -


Giancarlo R, Siragusa A, Siragusa E, Utro F "A basic analysis toolkit for biological sequences." Algorithms Mol Biol 2007
PMID: 17877802
PMCID: PMC2147010

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