Title: DASE2: differential alternative splicing variants estimation method without reference genome, and comparison with mapping strategy

Authors: Kouki Yonezawa; Keisuke Nakata; Ryuhei Minei; Atsushi Ogura

Addresses: Department of Computer Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829, Japan ' Department of Computer Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829, Japan ' Department of Computer Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829, Japan ' Department of Computer Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829, Japan

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 tissues and developmental processes in most organisms. This mechanism is well studied in model organisms so far but not in non-model organisms because the current standard method requires genomic sequences as well as fully annotated information of exons and introns. However, it is essential to uncover the landscape of alternative splicing of organisms to understand its evolutionary impacts and roles. Therefore, we developed a method for condition-specific alternative splicing estimation without reference genome based on de novo transcriptome assembly. We also tested estimation results of DASE with genome mapping method to infer reliability of our method, and displayed that detection level of alternative splicing can be comparable with mapping strategy and useful for the screening of condition specific alternative splicing in non-model organisms. The software is deposited to Github website.

Keywords: RNA-seq; isoforms; expression diversity.

DOI: 10.1504/IJDMB.2017.086101

International Journal of Data Mining and Bioinformatics, 2017 Vol.18 No.1, pp.56 - 73

Received: 26 Apr 2017
Accepted: 06 May 2017
Published online: 24 Aug 2017 *

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