Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes

  • Ilya Minkin
  • Anand Patel
  • Mikhail Kolmogorov
  • Nikolay Vyahhi
  • Son Pham
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8126)

Abstract

Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infectious diseases. In this paper, we present Sibelia, a tool for finding synteny blocks in multiple closely related microbial genomes using iterative de Bruijn graphs. Unlike most other tools, Sibelia can find synteny blocks that are repeated within genomes as well as blocks shared by multiple genomes. It represents synteny blocks in a hierarchy structure with multiple layers, each of which representing a different granularity level. Sibelia has been designed to work efficiently with a large number of microbial genomes; it finds synteny blocks in 31 S. aureus genomes within 31 minutes and in 59 E.coli genomes within 107 minutes on a standard desktop. Sibelia software is distributed under the GNU GPL v2 license and is available at: https://github.com/bioinf/Sibelia. Sibelia’s web-server is available at: http://etool.me/software/sibelia.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Ilya Minkin
    • 1
    • 2
  • Anand Patel
    • 1
    • 2
  • Mikhail Kolmogorov
    • 1
    • 2
  • Nikolay Vyahhi
    • 1
    • 2
  • Son Pham
    • 1
    • 2
  1. 1.Department of Computer Science and EngineeringUCSDLa JollaUSA
  2. 2.St. Petersburg Academic UniversitySt. PetersburgRussia

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