Home>Schools

  • Complex
  • Title
  • Author
  • Keyword
  • Abstract
  • Scholars
Search

[期刊]

ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference

Share
Edit Delete Claim

Author:

Yuan, Xiguo (Yuan, Xiguo.) | Xu, Xiangyan (Xu, Xiangyan.) | Zhao, Haiyong (Zhao, Haiyong.) | Unfold

Indexed by:

SCIE CPCI-S EI Web of Science

Abstract:

Next generation sequencing technology has led to the development of methods for the detection of novel sequence insertions (nsINS). Multiple signatures from short reads are usually extracted to improve nsINS detection performance. However, characterization of nsINSs larger than the mean insert size is still challenging. This article presents a new method, ERINS, to detect nsINS contents and genotypes of full spectrum range size. It integrates the features of structural variations and mapping states of split reads to find nsINS breakpoints, and then adopts a left-most mapping strategy to infer nsINS content by iteratively extending the standard reference at each breakpoint. Finally, it realigns all reads to the extended reference and infers nsINS genotypes through statistical testing on read counts. We test and validate the performance of ERINS on simulation and real sequencing datasets. The simulation experimental results demonstrate that it outperforms several peer methods with respect to sensitivity and precision. The real data application indicates that ERINS obtains high consistent results with those of previously reported and detects nsINSs over 200 base pairs that many other methods fail. In conclusion, ERINS can be used as a supplement to existing tools and will become a routine approach for characterizing nsINSs.

Keyword:

Bioinformatics Computer science extended reference Feature extraction Genomics genotypes insertion contents next-generation sequencing Novel sequence insertions Sensitivity Sequential analysis Tools

Author Community:

  • [ 1 ] [Yuan, Xiguo]Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China
  • [ 2 ] [Xu, Xiangyan]Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China
  • [ 3 ] [Zhao, Haiyong]Liaocheng Univ, Sch Comp Sci & Technol, Liaocheng 252000, Shandong, Peoples R China
  • [ 4 ] [Duan, Junbo]Xi An Jiao Tong Univ, Sch Life Sci & Technol, Key Lab Biomed Informat Engn, Minist Educ,Dept Biomed Engn, Xian 710049, Peoples R China

Reprint Author's Address:

Show more details

Source :

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

ISSN: 1545-5963

Year: 2021

Issue: 5

Volume: 18

Page: 1893-1901

3 . 0 1 5

JCR@2019

ESI Discipline: COMPUTER SCIENCE;

ESI HC Threshold:33

CAS Journal Grade:2

Cited Count:

WoS CC Cited Count: 0

30 Days PV: 1

FAQ| About| Online/Total:786/216906896
Address:XI'AN JIAOTONG UNIVERSITY LIBRARY(No.28, Xianning West Road, Xi'an, Shaanxi Post Code:710049) Contact Us:029-82667865
Copyright:XI'AN JIAOTONG UNIVERSITY LIBRARY Technical Support:Beijing Aegean Software Co., Ltd.