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MacLean, Daniel, Moulton, Vincent 
ORCID: https://orcid.org/0000-0001-9371-6435 and Studholme, David J.
(2010)
Finding sRNA generative locales from high-throughput sequencing data with NiBLS.
BMC Bioinformatics, 11.
ISSN 1471-2105
Abstract
Background: Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a paucity of methods for finding small RNA generative locales. Results: We describe and implement an algorithm that can determine small RNA generative locales from high-throughput sequencing data. The algorithm creates a network, or graph, of the small RNAs by creating links between them depending on their proximity on the target genome. For each of the sub-networks in the resulting graph the clustering coefficient, a measure of the interconnectedness of the subnetwork, is used to identify the generative locales. We test the algorithm over a wide range of parameters using RFAM sequences as positive controls and demonstrate that the algorithm has good sensitivity and specificity in a range of Arabidopsis and mouse small RNA sequence sets and that the locales it generates are robust to differences in the choice of parameters. Conclusions: NiBLS is a fast, reliable and sensitive method for determining small RNA locales in high-throughput sequence data that is generally applicable to all classes of small RNA.
| Item Type: | Article |
|---|---|
| Faculty \ School: | Faculty of Science > School of Computing Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre |
| Depositing User: | Vishal Gautam |
| Date Deposited: | 10 Mar 2011 10:33 |
| Last Modified: | 15 Jun 2023 23:47 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/22031 |
| DOI: | 10.1186/1471-2105-11-93 |
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