Analysis of sequence and secondary structure conservation of
MERS-CoV 5’-UTR.
GenBank at NCBI is the NIH genetic
sequence database that has compiled complete MERS-CoV genomes. 252
complete viral genomes were isolated from humans in 11 countries
including Saudi Arabia, United Arab Emirates, Jodan, Quatar, Oman,
Egypt, United Kingdom, USA, South Korea, Thailand, and China. 74
complete genomes were isolated from camels in Saudi Arabia and 132 from
dromedary camels in United Arab Emirates. The initial alignment of
sequence was performed using EMBL-EBI Clustal Omega
(https://www.ebi.ac.uk/Tools/msa/clustalo/). The most complete sequence
for 5’-UTR were further analyzed
using
LocARNA
program (11, 12)(http://rna.informatik.uni-freiburg.de/)
to determine the conservation of both sequence and secondary structure
of viral RNA. LocARNA performs simultaneous alignment and folding of
multiple RNAs. It implements the state-of-the-art light-weight alignment
algorithm with ensemble-based sparsification to improve the accuracy of
analysis.