In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles

Martin Bartas; Václav Brázda; Natália Bohálová; Alessio Cantara; Adriana Volná; Tereza Stachurová; Katerina Malachová; Eva B. Jagelská; Otília Porubiaková; Jirí Cerven; Petr Pecinka

All Nidovirales genomes were analyzed by the core of our Palindrome analyser webserver (Brázda et al., 2016) . The software was modified to read NCBI identifiers of sequences from text files. The size of IRs was set to 6-30 nt, size of spacers to 1-10 nt, and maximally one mismatch was allowed. A separate list of IRs in each of the 109 sequences and an overall report were exported. The overall report contained the lengths of the analyzed sequences, total number of IRs found, numbers of IRs grouped by size of IR (6-30 nt), and sum of IRs longer than 8 nt, 10 nt and 12 nt. The software also counted frequency of IRs in each sequence. Frequencies of IRs were normalized per 1,000 nt. Features tables of 109 Nidovirales genomes were downloaded from the NCBI database and grouped by their names as stated in the feature table file. Analyses of IRs occurrence inside and around (before and after) these features was performed. The search for IRs took place in predefined feature neighborhoods ± 100 nt around and inside feature boundaries. We calculated the numbers of all IRs and of those longer than 8, 10, and 12 nt in regions before, inside, and after the features.