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

CIDANE: Comprehensive isoform discovery and abundance estimation

Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
doi: https://doi.org/10.1101/017939
Stefan Canzar
1Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine
4Toyota Technological Institute at Chicago
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: canzar@ttic.edu
Sandro Andreotti
2Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Weese
2Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Knut Reinert
2Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gunnar W. Klau
3Life Sciences, Centrum Wiskunde & Informatica (CWI)
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts with significantly higher sensitivity and precision than existing tools, while competing in speed with the fastest methods. In addition to reconstructing transcripts ab initio, the algorithm also allows to make use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms. CIDANE supports the integrated analysis of RNA-seq and additional gene-boundary data and recovers splice junctions that are invisible to other methods. CIDANE is available at http://ccb.jhu.edu/software/cidane/.

Footnotes

  • ↵‡ Shared last author

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 April 12, 2015.
Download PDF

Supplementary Material

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.
CIDANE: Comprehensive isoform discovery and abundance estimation
(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
CIDANE: Comprehensive isoform discovery and abundance estimation
Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
bioRxiv 017939; doi: https://doi.org/10.1101/017939
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
CIDANE: Comprehensive isoform discovery and abundance estimation
Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
bioRxiv 017939; doi: https://doi.org/10.1101/017939

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 (4682)
  • Biochemistry (10360)
  • Bioengineering (7672)
  • Bioinformatics (26335)
  • Biophysics (13526)
  • Cancer Biology (10686)
  • Cell Biology (15438)
  • Clinical Trials (138)
  • Developmental Biology (8497)
  • Ecology (12821)
  • Epidemiology (2067)
  • Evolutionary Biology (16857)
  • Genetics (11399)
  • Genomics (15478)
  • Immunology (10617)
  • Microbiology (25216)
  • Molecular Biology (10222)
  • Neuroscience (54466)
  • Paleontology (401)
  • Pathology (1668)
  • Pharmacology and Toxicology (2897)
  • Physiology (4342)
  • Plant Biology (9247)
  • Scientific Communication and Education (1586)
  • Synthetic Biology (2558)
  • Systems Biology (6781)
  • Zoology (1466)