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A scoring matrix approach to detecting miRNA target sites
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 method...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2365947/ https://www.ncbi.nlm.nih.gov/pubmed/18377655 http://dx.doi.org/10.1186/1748-7188-3-3 |
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author | Moxon, Simon Moulton, Vincent Kim, Jan T |
author_facet | Moxon, Simon Moulton, Vincent Kim, Jan T |
author_sort | Moxon, Simon |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2365947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-23659472008-05-05 A scoring matrix approach to detecting miRNA target sites Moxon, Simon Moulton, Vincent Kim, Jan T Algorithms Mol Biol Research 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. BioMed Central 2008-03-31 /pmc/articles/PMC2365947/ /pubmed/18377655 http://dx.doi.org/10.1186/1748-7188-3-3 Text en Copyright © 2008 Moxon et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Moxon, Simon Moulton, Vincent Kim, Jan T A scoring matrix approach to detecting miRNA target sites |
title | A scoring matrix approach to detecting miRNA target sites |
title_full | A scoring matrix approach to detecting miRNA target sites |
title_fullStr | A scoring matrix approach to detecting miRNA target sites |
title_full_unstemmed | A scoring matrix approach to detecting miRNA target sites |
title_short | A scoring matrix approach to detecting miRNA target sites |
title_sort | scoring matrix approach to detecting mirna target sites |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2365947/ https://www.ncbi.nlm.nih.gov/pubmed/18377655 http://dx.doi.org/10.1186/1748-7188-3-3 |
work_keys_str_mv | AT moxonsimon ascoringmatrixapproachtodetectingmirnatargetsites AT moultonvincent ascoringmatrixapproachtodetectingmirnatargetsites AT kimjant ascoringmatrixapproachtodetectingmirnatargetsites AT moxonsimon scoringmatrixapproachtodetectingmirnatargetsites AT moultonvincent scoringmatrixapproachtodetectingmirnatargetsites AT kimjant scoringmatrixapproachtodetectingmirnatargetsites |