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miRBase and deep-seq data: paper published in NAR

A manuscript describing the integration of deep sequencing data in miRBase is now available in Nucleic Acids Research (Database Issue, Advance Access).

Ana Kozomara and Sam Griffiths-Jones.
miRBase: integrating microRNA annotation and deep-sequencing data.
Nucleic Acids Res. (2010)
doi: 10.1093/nar/gkq1027

Posted in papers.

5 Responses

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  1. Francis Nunes says

    I´m looking for published studies showing a gene silencing followed by microRNA microarrays approach. In other words, the effects of a gene knockdown on the general miRNA profiles. Could you help me?

  2. sam says

    I’m afraid I don’t know of anything specific, but I’m sure some such data will be out there. You might be able to identify some from trawling the GEO database.

    • Francis Nunes says

      Good idea. I´ll search at GEO. Thanks.

  3. Jay says

    Hi, Sam:
    Great site!
    I am searching a bacterial genome (40K bp) for the presence of target sites for the human miRNAs. As the max size for sequence is only 1000bps, wondering if searching <1000bps is the only way we can do? Thanks a lot! Jay

  4. sam says

    Through the website, yes. But you can easily download blast from the NCBI site, and the hairpin or mature miRNA sets from miRBase, and run the searches yourself on your own machine.

    (The miRBase sequence search page is *NOT* designed to predict miRNA targets, because blast and ssearch are probably not the right tools to use for target prediction. You might prefer to use one of the bespoke target prediction tools. The miRBase search page is setup to facilitate identification of miRNA homologs.)