Detection of orthologous exons and isoforms using EGIO

Jinfa Ma, Jane Y. Wu*, Li Zhu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Motivation: Alternative splicing is an important mechanism to generate transcriptomic and phenotypic diversity. Existing methods have limited power to detect orthologous isoforms. Results: We develop a new method, EGIO, to detect orthologous exons and orthologous isoforms from two species. EGIO uses unique exonic regions to construct exon groups, in which process dynamic programming strategy is used to do exon alignment. EGIO could cover all the coding exons within orthologous genes. A comparison between EGIO and ExTraMapper shows that EGIO could detect more orthologous isoforms with conserved sequence and exon structures. We apply EGIO to compare human and chimpanzee protein-coding isoforms expressed in the frontal cortex and identify 6912 genes that express human unique isoforms. Unexpectedly, more human unique isoforms are detected than those conserved between humans and chimpanzees. Availability and implementation: Source code and test data of EGIO are available at https://github.com/wu-lab-egio/ EGIO.

Original languageEnglish (US)
Pages (from-to)4474-4480
Number of pages7
JournalBioinformatics
Volume38
Issue number19
DOIs
StatePublished - Oct 1 2022

ASJC Scopus subject areas

  • Computational Mathematics
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability
  • Computer Science Applications
  • Computational Theory and Mathematics

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