A novel algorithm for detecting co-evolutionary domains in protein and nucleotide sequences

Xiaoyu Zhang, Xiangke Liao, Hao Zhu*, Kenli Li, Benyun SHI, Shaoliang Peng

*Corresponding author for this work

Research output: Chapter in book/report/conference proceedingConference contributionpeer-review

Abstract

Co-evolution exists ubiquitously in biological systems. At the molecular level, interacting proteins, such as ligands and their receptors and components in protein complexes, co-evolve to maintain their structural and functional interactions. Many proteins contain multiple functional domains interacting with different partners, making co-evolution of interacting domains occur more prominently. Multiple methods have been developed to predict interacting proteins or domains within proteins by detecting their co-variation. This strategy neglects the fact that interacting domains can be highly co-conserved due to their functional interactions. Here we report a novel algorithm to detect signals of both co-positive selection (co-variation) and co-purifying selection (co-conservation). Preliminary results show that our algorithm performs well and outperforms the popular co-variation analysis program CAPS. Our algorithm can be widely used to predict interacting domains in protein and nucleotide sequences and to analyze protein-ncRNA complexes.

Original languageEnglish
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages56-61
Number of pages6
ISBN (Electronic)9781509030491
DOIs
Publication statusPublished - 15 Dec 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: 13 Nov 201716 Nov 2017

Publication series

NameProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume2017-January

Conference

Conference2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/TerritoryUnited States
CityKansas City
Period13/11/1716/11/17

Scopus Subject Areas

  • Biomedical Engineering
  • Health Informatics

User-Defined Keywords

  • coevolution
  • evolution
  • positive selection
  • purifying selection

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