Prediction of ncRNA and CpG islands

SS Shuai Sun
YW Yue Wang
WZ Wenhong Zeng
XD Xiao Du
LL Lei Li
XH Xiaoning Hong
XH Xiaoyun Huang
HZ He Zhang
MZ Mengqi Zhang
GF Guangyi Fan
XL Xin Liu
SL Shanshan Liu
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Four types of ncRNA (Non-coding RNA), including tRNA, snRNA, miRNA, and rRNA were predicted. We used tRNAscan-SE (v1.3.1) to predict tRNA in our genome with default parameters. The genome was aligned against Rfam (v12.0) database (Nawrocki E P et al., 2015) and based on mapping results we used infernal (v1.1.1) (Nawrocki E P & Eddy S R, 2013) to infer snRNA and miRNA. We aligned vertebrate rRNA database against Mekong tiger perch genome to predict rRNA.

The CpG islands (CGIs), which are clusters of CpGs in CG-rich regions, were identified on genome wide using CpGIScan52 with the parameters “–length 500–gcc 55–oe 0.65”.

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