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Ortholog Detection Using the Reciprocal Smallest Distance Algorithm

  • Protocol
Comparative Genomics

Part of the book series: Methods In Molecular Biology™ ((MIMB,volume 396))

Summary

All protein coding genes have a phylogenetic history that when understood can lead to deep insights into the diversification or conservation of function, the evolution of developmental complexity, and the molecular basis of disease. One important part to reconstructing the relationships among genes in different organisms is an accurate method to find orthologs as well as an accurate measure of evolutionary diversification. The present chapter details such a method, called the reciprocal smallest distance algorithm (RSD). This approach improves upon the common procedure of taking reciprocal best Basic Local Alignment Search Tool hits (RBH) in the identification of orthologs by using global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes. RSD finds many putative orthologs missed by RBH because it is less likely to be misled by the presence of close paralogs in genomes. The package offers a tremendous amount of flexibility in investigating parameter settings allowing the user to search for increasingly distant orthologs between highly divergent species, among other advantages. The flexibility of this tool makes it a unique and powerful addition to other available approaches for ortholog detection.

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Acknowledgments

Many thanks to past and present members of the Computational Biology Initiative who provided advice and expertise, I-Hsien Wu, Tom Monaghan, Jian Pu, Saurav Singh, and Leon Peshkin. This material is based upon work supported by the National Science Foundation under Grant No. DBI 0543480.

Author information

Authors and Affiliations

  1. Department of Systems Biology, Harvard Medical School, Harvard

    Dennis P. Wall

  2. Department of Systems Biology, Harvard Medical School, USA

    Todd DeLuca

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  1. Dennis P. Wall
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  2. Todd DeLuca
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Editor information

Editors and Affiliations

  1. Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI

    Nicholas H. Bergman

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© 2007 Humana Press Inc.

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Wall, D.P., DeLuca, T. (2007). Ortholog Detection Using the Reciprocal Smallest Distance Algorithm. In: Bergman, N.H. (eds) Comparative Genomics. Methods In Molecular Biology™, vol 396. Humana Press. https://doi.org/10.1007/978-1-59745-515-2_7

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  • DOI: https://doi.org/10.1007/978-1-59745-515-2_7

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-934115-37-4

  • Online ISBN: 978-1-59745-515-2

  • eBook Packages: Springer Protocols

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