Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection

Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu, Yufeng Wu
doi: https://doi.org/10.1101/134411
Xin Li
Computer Science & Engineering Dept., University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chong Chu
Computer Science & Engineering Dept., University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jingwen Pei
Computer Science & Engineering Dept., University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ion Măndoiu
Computer Science & Engineering Dept., University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yufeng Wu
Computer Science & Engineering Dept., University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

While RNA is often created from linear splicing during transcription, recent studies have found that non-canonical splicing sometimes occurs. Non-canonical splicing joins 3’ and 5’ and forms the socalled circular RNA. It is now believed that circular RNA plays important biological roles such as affecting susceptibility in some diseases. within these few years, several experimental methods have been developed to enrich circular RNA while degrade linear RNA. Although several useful software tools for circRNA detection have been developed as well, these tools may miss many circular RNA. Also, existing tools are slow for large data because those tools often depend on reads mapping. In this paper, we present a new computational approach, named CircMarker, based on k-mers rather than reads mapping for circular RNA detection. CircMarker takes advantage of transcriptome annotation files to create k-mer table for circular RNA detection. Empirical results show that CircMarker outperforms existing tools in circular RNA detection on accuracy and efficiency in many simulated and real datasets. CircMarker can be downloaded from https://github.com/lxwgcool/CircMarker.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted May 05, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection
Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu, Yufeng Wu
bioRxiv 134411; doi: https://doi.org/10.1101/134411
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection
Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu, Yufeng Wu
bioRxiv 134411; doi: https://doi.org/10.1101/134411

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3606)
  • Biochemistry (7580)
  • Bioengineering (5529)
  • Bioinformatics (20808)
  • Biophysics (10335)
  • Cancer Biology (7986)
  • Cell Biology (11645)
  • Clinical Trials (138)
  • Developmental Biology (6610)
  • Ecology (10214)
  • Epidemiology (2065)
  • Evolutionary Biology (13625)
  • Genetics (9545)
  • Genomics (12851)
  • Immunology (7925)
  • Microbiology (19553)
  • Molecular Biology (7668)
  • Neuroscience (42128)
  • Paleontology (308)
  • Pathology (1258)
  • Pharmacology and Toxicology (2203)
  • Physiology (3268)
  • Plant Biology (7045)
  • Scientific Communication and Education (1294)
  • Synthetic Biology (1951)
  • Systems Biology (5428)
  • Zoology (1118)