miRNAminer: a tool for homologous microRNA gene search
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1471-2105-9-39.pdf
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498.09 KB
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Checksum (MD5)
09b0c7ee4bff4b1733a33e981b709ab2
Author(s)
Artzi, Shay
Kiezun, Adam
Shomron, Noam
Date Issued
January 2008
Journal
BMC Bioinformatics
Publisher
BioMed Central Ltd
Citation
Artzi, Shay, Adam Kiezun, and Noam Shomron. “miRNAminer: A tool for homologous microRNA gene search.” BMC Bioinformatics 9.1 (2008): 39.
Version
Final published version
Abstract
Background MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental and computational methods were used to construct miRNA gene repositories agreeing with careful submission guidelines. Results An algorithm we developed – miRNAminer – is used for homologous conserved miRNA gene search in several animal species. Given a search query, candidate homologs from different species are tested for their known miRNA properties, such as secondary structure, energy and alignment and conservation, in order to asses their fidelity. When applying miRNAminer on seven mammalian species we identified several hundreds of high-confidence homologous miRNAs increasing the total collection of (miRbase) miRNAs, in these species, by more than 50%. miRNAminer uses stringent criteria and exhibits high sensitivity and specificity. Conclusion We present – miRNAminer – the first web-server for homologous miRNA gene search in animals. miRNAminer can be used to identify conserved homolog miRNA genes and can also be used prior to depositing miRNAs in public databases. miRNAminer is available at http://pag.csail.mit.edu/mirnaminer.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/1471-2105-9-39
