Original Article | 2013, Vol.35, No.2, pp. 143-148
Computational identification of Penaeus monodon microRNA genes and their targets
Pitipol Meemak, Amornrat Phongdara, Wilaiwan Chotigeat and Martti T. Tammi
pp. 143 - 148
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 developed a computational workflow to identify conserved miRNA genes in the 10,536 unique Penaeus monodon expressed sequence tags (ESTs). After removing all simple repeats and coding regions in the ESTs, the workflow uses both the conservation of miRNA sequences and several filters obtained from pre-miRNA secondary structure properties to identify conserved miRNAs. Finally, we discovered six potential conserved miRNA genes such as mir-4152, mir-466k, miR-32*, lin-4, mir-1346 and mir-4310.
