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  • #1

    How to predicate miRNA target without a reference genome

    Hi, guys

    I am trying to predicate miRNA target from a fish species. I have sequenced small RNA and mRNA and then proceed to do the de novo assembly to get the transcriptome. There is no whole genome sequence available for this fish. Any idea about how to predicate the miRNA target without genome sequence and degradome? Thank you so much!
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  • #2
    Hi
    I have recently read about miReader but I havent used it but as much as I have read it works good for non-model organism.
    miReader: Discovering Novel miRNAs in Species without Sequenced Genome
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066857
    Along with computational approaches, NGS led technologies have caused a major impact upon the discoveries made in the area of miRNA biology, including novel miRNAs identification. However, to this date all microRNA discovery tools compulsorily depend upon the availability of reference or genomic sequences. Here, for the first time a novel approach, miReader, has been introduced which could discover novel miRNAs without any dependence upon genomic/reference sequences. The approach used NGS read data to build highly accurate miRNA models, molded through a Multi-boosting algorithm with Best-First Tree as its base classifier. It was comprehensively tested over large amount of experimental data from wide range of species including human, plants, nematode, zebrafish and fruit fly, performing consistently with >90% accuracy. Using the same tool over Illumina read data for Miscanthus, a plant whose genome is not sequenced; the study reported 21 novel mature miRNA duplex candidates. Considering the fact that miRNA discovery requires handling of high throughput data, the entire approach has been implemented in a standalone parallel architecture. This work is expected to cause a positive impact over the area of miRNA discovery in majority of species, where genomic sequence availability would not be a compulsion any more.

    Hope it helps.

    Comment

    • #3
      Hi,
      Thank you so much. I will try and let you know the results.

      Comment

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