Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data

Ragan, Chikako, Mowry, Bryan J. and Bauer, Denis C. (2012) Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data. Nucleic Acids Research, 40 16: 7633-7643. doi:10.1093/nar/gks505


Author Ragan, Chikako
Mowry, Bryan J.
Bauer, Denis C.
Title Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
1362-4962
Publication date 2012-09
Sub-type Article (original research)
DOI 10.1093/nar/gks505
Open Access Status DOI
Volume 40
Issue 16
Start page 7633
End page 7643
Total pages 11
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2013
Language eng
Abstract Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference- genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present NORAHDESK, the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. NORAHDESK utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with DARIO and MIRDEEP2 and found that NORAHDESK produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes First published online: June 16 2012.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Brain Institute Publications
Official 2013 Collection
 
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Created: Wed, 11 Jul 2012, 11:58:07 EST by Debra McMurtrie on behalf of Queensland Brain Institute