DASE: Condition-specific differential alternative splicing variants estimation method without reference genome sequence, and its application to non-model organisms

Abstract

Alternative splicing is a mechanism to produce gene expression diversity under the constraint of a limited number of genes, causing spatiotemporal gene expression in many tissues and developmental processes in organisms. This mechanism is well studied in model organisms but not in non-model organisms because the current standard method requires genomic sequences as well as fully annotated information of exons and introns, that are not accessible from non-model organisms. However, it is essential to uncover the landscape of alternative splicing of organisms to understand its evolutionary impacts and roles. We developed a method for condition-specific alternative splicing estimation based on de novo transcriptome assembly, and it would help to enlarge knowledge of alternative splicing functionalized in non-model organisms. The software is deposited to https://github.com/koukiyonezawa/DASE.