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IsoDetect: Detection of splice isoforms from third generation long reads based on short feature sequences

Author(s):

Hongdong Li, Wenjing Zhang , Yuwen Luo and Jianxin Wang *  

Abstract:


Aims:Accurately detect isoforms from third generation sequencing data.

Background: Transcriptome annotation is the basis for the analysis of gene expression and regulation. The transcriptome annotation of many organisms such as humans is far from incomplete, due partly to the challenge in the identification of isoforms that are produced from the same gene through alternative splicing. Third generation sequencing (TGS) reads provide unprecedented opportunity for detecting isoforms due to their long length that exceeds the length of most isoforms. One limitation of current TGS reads-based isoform detection methods is that they are exclusively based on sequence reads, without incorporating the sequence information of known isoforms.

Objective: Develop an efficient method for isoform detection.

Method: Based on annotated isoforms, we propose a splice isoform detection method called IsoDetect. First, the sequence at exon-exon junction is extracted from annotated isoforms as the “short feature sequence”, which is used to distinguish different splice isoforms. Second, we aligned these feature sequences to long reads and divided long reads into groups that contain the same set of feature sequences, thereby avoiding the pair-wise comparison among the large number of long reads. Third, clustering and consensus generation are carried out based on sequence similarity. For the long reads that do not contain any short feature sequence, clustering analysis based on sequence similarity is performed to identify isoforms.

Result: Tested on two datasets from Calypte Anna and Zebra Finch, IsoDetect showed higher speed and compelling accuracy compared with four existing methods.

Conclusion: IsoDetect is a promising method for isoform detection.

Other: This paper was accepted by the CBC2019 conference.

Keywords:

isoform detection, sequencing technologies, third generation sequencing, transcriptome.

Affiliation:

Central South University, School of Computer Science and Engineering, Central South University, School of Computer Science and Engineering, Central South University, School of Computer Science and Engineering , Central South University, School of Computer Science and Engineering



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