2.9 Prediction of non-coding RNA
We annotated tRNA, rRNA, snRNA, and miRNAs across the assembled genome
sequence. Non-coding RNA sequence was predicted using tRNAscan-SE
1.3.1(Lowe et al., 1997) (http://lowelab.ucsc.edu/tRNAscan-SE/) based on
the RNA structure. The rRNA sequences in the Chinese walnut genome were
predicted using BLASTN to search for conserved characteristics with
related species such as J. regia . The miRNA and snRNA in the
assembled Chinese walnut genome were identified using INFERNAL software
(Nawrocki and Eddy, 2013) against the Rfam 13.0 database
(Griffiths-Jones et al., 2005).