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OMG! Orthologs for Multiple Genomes - Competing Formulations

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Bioinformatics Research and Applications (ISBRA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6674))

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Abstract

Multiple alignment of the gene orders in sequenced genomes is an important problem in comparative genomics [1]. A key aspect is the construction of disjoint orthology sets of genes, in which each element is orthologous to all other genes (on different genomes) in the same set. Approaches differ as to the nature and timing and relative importance of sequence alignment, synteny block construction, and paralogy resolution in constructing these sets.

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References

  1. Fostier, J., et al.: A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinformatics 27, 749–756 (2011)

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  2. Lyons, E., Freeling, M.: How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 53, 661–673 (2008)

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  3. Lyons, E., et al.: Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Phys. 148, 1772–1781 (2008)

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  5. Zheng, C., Sankoff, D.: Gene order in Rosid phylogeny, inferred from pairwise syntenies among extant genomes. In: Chen, J., Wang, J., Zelikovsky, A. (eds.) ISBRA 2011. LNCS (LNBI), vol. 6674, pp. 99–110. Springer, Heidelberg (2011)

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Author information

Authors and Affiliations

  1. Department of Mathematics and Statistics, University of Ottawa, Canada

    David Sankoff

Authors
  1. David Sankoff
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, 77843-3112, College Station, TX, USA

    Jianer Chen

  2. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

  3. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Alexander Zelikovsky

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© 2011 Springer-Verlag Berlin Heidelberg

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Sankoff, D. (2011). OMG! Orthologs for Multiple Genomes - Competing Formulations. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_2

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  • DOI: https://doi.org/10.1007/978-3-642-21260-4_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21259-8

  • Online ISBN: 978-3-642-21260-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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