id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-000895-z5rdf0mi	Belalov, Ilya S.	Causes and Implications of Codon Usage Bias in RNA Viruses	2013-02-25		.txt	text/plain	5449	272	45	A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. A general rationale for analyzing impact of (di)nucleotide bias on ENC is randomizing or shuffling synonymous codons in the original genome sequence whilst preserving the factor under study [37] . Unfortunately, common statistical tests were poorly applicable to this approach, because all factors that affect codon preference (e.g. structural RNA elements) could not be accounted for, and therefore even a negligible difference in ENC between the original and generated sequences (e.g. 0.2 SD) passed a formal significance test upon increasing the number of replicates. Overall, dN 23 and dN 231 shuffling produced ENC values that differed from the original sequence by less than one in 25 of 29 viruses, indicating that we explored almost all types of pressure that affect overall codon usage.	./cache/cord-000895-z5rdf0mi.txt	./txt/cord-000895-z5rdf0mi.txt