A planarian nidovirus expands the limits of RNA genome size

Amir Saberi; Anastasia A. Gulyaeva; John L. Brubacher; Phillip A. Newmark; Alexander E. Gorbalenya

Computational protein and RNA sequence analyses. Virus protein sequences were analyzed to predict disordered regions (DisEMBL 1.5 (73)), transmembrane regions (TMHMM v.2.0), secondary structure (Jpred4 (74)), signal peptides (SignalP 4.1 (75) ), Nglycosylation sites (NetNGlyc 1.0) and furin cleavage sites (ProP 1.0 (76)). To identify sites enriched with amino acid residue, distribution of each residue along polyprotein sequence was assessed using permutation test executed with a custom R script. Generation of multiple sequence alignments of RNA virus proteins was facilitated by Viralis platform (77) . Protein homology profile-based analyses were assisted with HMMER 3.1 (78) , and HH-suite 2.0.16 (79) . To predict RNA secondary structure and PRF sites we used Mfold web server (80) and KnotInFrame (81), respectively. Blastn (BLAST+ v2.2.29) (56) was used to identify RNA repeats.