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Overview

NorahDesk is a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data. NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes.

It does this by

  1. Merging all overlapping reads into one longer sequence fragment (a contig).
  2. Hybridizing closely located contigs to each other.
  3. Merging overlapping newly created transcripts and original contigs to create the final reconstructed transcripts.
  4. Compute the folding energies of remaining transcripts and discard the transcripts with high free energy.

NorahDesk is particularly suitable for the prediction of piRNAs as it is the first program to "annotate by association": if novel transcripts form a thermodynamically stable secondary structure with already known piRNA transcripts, it is likely that the unannotated contigs are also piRNAs. Shown in the image below: Contig2 and Contig3 do not overlap with any known annotations while all other contigs in this cluster overlap with known piRNAs.

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Implementation

NorahDesk is implemented in Java. It requires two external programs: BEDTOOLS and Vienna RNA Package.
The program is tested only on Mac OS X and Linux platforms.

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Download

NorahDesk v1.4 with Vienna RNA version 2

Older versions:

NorahDesk v1.3 with Vienna RNA version 2

NorahDesk v1.2 with Vienna RNA version 1

Description of NorahDesk

Sample data set

Mouse chromosome sequences

Annotation files:

Mouse (mm10) annotation file

Human (hg19) annotation file

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Citation

Ragan C., Mowry B., Bauer D.C. Hybridization based reconstruction of small non-coding RNA transcripts from deep sequencing data.

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Contact

Inquiries to c.ragan@uq.edu.au

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Last modified: Fri July 26 2013

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