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Long-term trends in evolution of indels in protein sequences

BMC Evolutionary Biology
Springer (Biomed Central Ltd.)
Publication Date
DOI: 10.1186/1471-2148-7-19
  • Research Article
  • Biology

Abstract ral ss BioMed CentBMC Evolutionary Biology Open AcceResearch article Long-term trends in evolution of indels in protein sequences Yuri Wolf1, Thomas Madej1, Vladimir Babenko2, Benjamin Shoemaker1 and Anna R Panchenko*1 Address: 1National Center for Biotechnology Information, National Institutes of Health, Bethesda, 20894, US and 2Institute of Cytology and Genetics, Novosibirsk, Russia Email: Yuri Wolf - [email protected]; Thomas Madej - [email protected]; Vladimir Babenko - [email protected]; Benjamin Shoemaker - [email protected]; Anna R Panchenko* - [email protected] * Corresponding author Abstract Background: In this paper we describe an analysis of the size evolution of both protein domains and their indels, as inferred by changing sizes of whole domains or individual unaligned regions or "spacers". We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups. Results: We found that more than one third of all domains have a statistically significant tendency to increase/decrease in size in evolution as judged from the overall domain size distribution as well as from the size distribution of individual spacers. Moreover, the fraction of domains and individual spacers increasing in size is almost twofold larger than the fraction decreasing in size. Conclusion: We showed that the tolerance to insertion and deletion events depends on the domain's taxonomy span. Eukaryotic domains are depleted in insertions compared to the overall test set, namely, the number of spacers increasing in size is about the same as the number of spacers decreasing in size. On the other hand, ancient domain families show some bias towards insertions or spacers which grow in size in evolution. Domains from several Gene Ontology categories also demonstrate certain tendencies for insertion or deletion events as inferred from the analysis of spacer sizes. Background Proteins evolve th

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