id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-102968-mhawyect	Desirò, Daniel	SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs	2018-09-23		.txt	text/plain	4044	233	58	Results Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate destructive and compensatory mutants of two interacting single-stranded RNAs. This will facilitate a fast and accurate assessment of key regions, possibly involved in functional long-range RNA-RNA interactions and finally help virologists to design appropriate experiments. In this study, we present a tool called SilentMutations (SIM) that effectively simulates synonymous (silent) compensatory mutations in two single-stranded viral RNAs and is therefore appropriate for the in vitro assessment of predicted LRIs. Here, we present a command-line tool, called SilentMutations (SIM), that can simulate synonymous structure-destroying and structurepreserving mutation pairs within coding regions for long-range RNA-RNA interaction experiments. Figure 1 : Overall workflow of the SilentMutations tool, exemplary shown for two sequences from a negative single-stranded RNA virus genome (ssRNA-) (a) The first step will extract the defined range in each sequence and possibly increase the range to preserve codons in the given reading frame.	./cache/cord-102968-mhawyect.txt	./txt/cord-102968-mhawyect.txt