A scoring matrix approach to detecting miRNA target sites

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Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Kim, Jan T. (2008) A scoring matrix approach to detecting miRNA target sites. Algorithms for Molecular Biology, 3 (3). ISSN 1748-7188

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Abstract

Background Experimental identification of microRNA (miRNA) targets is a difficult and time consuming process. As a consequence several computational prediction methods have been devised in order to predict targets for follow up experimental validation. Current computational target prediction methods use only the miRNA sequence as input. With an increasing number of experimentally validated targets becoming available, utilising this additional information in the search for further targets may help to improve the specificity of computational methods for target site prediction. Results We introduce a generic target prediction method, the Stacking Binding Matrix (SBM) that uses both information about the miRNA as well as experimentally validated target sequences in the search for candidate target sequences. We demonstrate the utility of our method by applying it to both animal and plant data sets and compare it with miRanda, a commonly used target prediction method. Conclusion We show that SBM can be applied to target prediction in both plants and animals and performs well in terms of sensitivity and specificity. Open source code implementing the SBM method, together with documentation and examples are freely available for download from the address in the Availability and Requirements section.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	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 > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Related URLs:	http://dx.doi.org/10.1186/1748-7188-3-3
Depositing User:	EPrints Services
Date Deposited:	01 Oct 2010 13:41
Last Modified:	24 Sep 2024 09:29
URI:	https://ueaeprints.uea.ac.uk/id/eprint/3035
DOI:	10.1186/1748-7188-3-3

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