PMC:7067204 / 7105-8880
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7067204","sourcedb":"PMC","sourceid":"7067204","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7067204","text":"Genome characterization and phylogenetic analysis\nPhylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees [12]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) was shown next to the branches [13]. The tree was drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and were in the units of the number of amino acid substitutions per site [14]. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Evolutionary analyses were conducted in MEGA X [15]. Multiple alignment was performed using CLUSTAL 2.1 and further visualized using BOXSHADE 3.21. Structural analysis of orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED) [16]. For the prediction of protein secondary structure including beta sheet, alpha helix, and coil, initial amino acid sequences were input and analysed using neural networking and its own algorithm. Predicted structures were visualized and highlighted on the BOXSHADE alignment. Prediction of transmembrane domains was performed using the TMHMM 2.0 server (http://www.cbs.dtu.dk/services/TMHMM/). Secondary structure prediction in the 5′-untranslated region (UTR) and 3′-UTR was performed using the RNAfold WebServer (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi) with minimum free energy (MFE) and partition function in Fold algorithms and basic options. The human SARS-CoV 5′- and 3′- UTR were used as references to adjust the prediction 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