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RECOMB Workshop on Comparative Genomics

RCG 2004: Comparative Genomics pp 72–84Cite as

Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3388))

Abstract

We describe a new method for reliably identifying conserved segments among genome sequences that have undergone rearrangement, horizontal transfer, and substantial nucleotide-level divergence. A Gibbs-like sampler explores different combinations of sequence-based markers shared by the genomes under study. The sampler assigns each marker a posterior probability based on how frequently it participates in some collinear group of markers. Markers with high p.p. values are likely members of conserved segments. The method identifies both large-scale and local trends in segmental collinearity, providing suitable input for genome alignment and rearrangement history inference tools. Applying our method to genomes of four Streptococci reveals that rearranged segments in these organisms belong in two size categories: large conserved segments that are interrupted by a staccato of single gene or operon-size small segments. The rearrangement pattern of large segments is best explained by symmetric inversions about the origin of replication while the pattern of small segments is not.

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Author information

Authors and Affiliations

  1. Dept. of Animal Health and Biomedical Sciences, University of Wisconsin – Madison, 1656 Linden Dr., Madison, WI, 53706, USA

    Bob Mau, Aaron E. Darling & Nicole T. Perna

  2. Dept. of Oncology, University of Wisconsin – Madison, 1656 Linden Dr., Madison, WI, 53706, USA

    Bob Mau

  3. Dept. of Computer Science, University of Wisconsin – Madison, 1656 Linden Dr., Madison, WI, 53706, USA

    Aaron E. Darling

  4. The Genome Center of Wisconsin, University of Wisconsin – Madison, 1656 Linden Dr., Madison, WI, 53706, USA

    Nicole T. Perna

Authors
  1. Bob Mau
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  2. Aaron E. Darling
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  3. Nicole T. Perna
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Editor information

Editors and Affiliations

  1. KTH, Royal Institute of Technology, Stockholm, Sweden

    Jens Lagergren

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© 2005 Springer-Verlag Berlin Heidelberg

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Mau, B., Darling, A.E., Perna, N.T. (2005). Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes. In: Lagergren, J. (eds) Comparative Genomics. RCG 2004. Lecture Notes in Computer Science(), vol 3388. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32290-0_6

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  • DOI: https://doi.org/10.1007/978-3-540-32290-0_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-24455-4

  • Online ISBN: 978-3-540-32290-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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