Detection of orthologous exons and isoforms using EGIO

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 Source code and test data of EGIO are available at https://github.com/wu-lab-egio/EGIO. Supplementary information Supplementary data are available at Bioinformatics online.

SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies

“…However, estimating the evolutionary history of transcripts remains difficult [ 7 – 9 ], and evaluating computational methods developed for this task requires gold standard data. The latter is also needed for the experimental assessment of methods developed for the analysis of spliced RNA sequences, such as splice site prediction [ 12 , 13 ], identification of homologous exons [ 5 , 14 ], spliced alignment [ 15 , 16 ], multiple sequence alignment [ 17 , 18 ], or splicing orthology inference [ 19 ]. In the absence of real gold standard data, there is a need for simulation tools to generate synthetic data.…”