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Computational identification of Penaeus monodon microRNA genes and their targets

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Author(s): Pitipol Meemak | Amornrat Phongdara | Wilaiwan Chotigeat | Martti T. Tammi

Journal: Songklanakarin Journal of Science and Technology
ISSN 0125-3395

Volume: 35;
Issue: 2;
Start page: 143;
Date: 2013;
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Keywords: Penaeus monodon | miRNAs | MicroRNAs | expressed sequence tags | ESTs

ABSTRACT
MicroRNAs (miRNAs) are a distinct class of small non-coding RNAs, ~22 nt long, found in a wide variety of organisms.They play important regulatory roles by silencing gene activities at the post-transcriptional level. In this work, we developeda computational workflow to identify conserved miRNA genes in the 10,536 unique Penaeus monodon expressed sequencetags (ESTs). After removing all simple repeats and coding regions in the ESTs, the workflow uses both the conservationof miRNA sequences and several filters obtained from pre-miRNA secondary structure properties to identify conservedmiRNAs. Finally, we discovered six potential conserved miRNA genes such as mir-4152, mir-466k, miR-32*, lin-4, mir-1346 andmir-4310.
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