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Oh Brother, Where Art Thou? Finding Orthologs in the Twilight and Midnight Zones of Sequence Similarity

  • Bianca Hermine Habermann
Chapter

Abstract

Inferring remote orthologs is a persistent challenge in computational biology. The identification of orthologs is necessary for performing evolutionary analyses, comparative genomics, and genome annotation or for functional predictions and sensible planning of experimental studies. If we miss orthologous relationships due to low sequence conservation, we lose a significant amount of information. Given their fast evolutionary rates, remote orthologs can only be identified on protein level. A pair of proteins that has evolved by speciation and has below 30 % sequence identity can be defined as remote orthologs. Their high sequence divergence prevents their unambiguous recognition as orthologous proteins and does not allow a reliable interpretation of their evolutionary relationship. Thus, many remote orthologs remain hidden to date. In this article, I review current methods for remote orthology inference, highlight existing problems in, and discuss potential solutions for discovering remote orthologs.

Keywords

Hide Markov Model Orthologous Relationship Orthology Assignment Large Evolutionary Distance Remote Homology Detection 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

I would like to thank Frank Schnorrer and Friedhelm Pfeiffer for critical reading of the manuscript. This work was supported by the Max Planck Society and by the CNRS.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Max Planck Institute of BiochemistryMartinsriedGermany
  2. 2.Aix Marseille Université CNRSMarseilleFrance

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