Identifying small interfering RNA loci from high-throughput sequencing data.

[admin]

Identifying small interfering RNA loci from high-throughput sequencing data.

Bioinformatics. 2011 Dec 9;

Authors: Hardcastle TJ, Kelly KA, Baulcombe DC

Abstract
MOTIVATION: Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterisation of the precursors from which they are derived. RESULTS: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from mutliple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated data sets. AVAILABILITY: Our methods are available as the Bioconductor (www.bioconductor.org) package segmentSeq (version 1.5.6 and above). CONTACT: tjh48@cam.ac.uk.


PMID: 22171331 [PubMed - as supplied by publisher]



PubMed comprises more than 19 million citations for biomedical articles from MEDLINE and life science journals. This RSS feed searches for mentions of Bioconductor - the open source and open development software project for the analysis and comprehension of genomic data.
More from PubMed...