id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-002758-d86hnox1	Opuu, Vaitea	Computational design of fully overlapping coding schemes for protein pairs and triplets	2017-11-20		.txt	text/plain	5501	303	64	We have examined the possibility to encode an arbitrary pair of protein domains as a dual gene, with the shorter coding sequence completely embedded in the longer one. An example of a designed overlapping gene was produced recently, where each DNA strand coded for a simplified but functional aminoacyl-tRNA synthetase "Urzyme" [13] [14] [15] [16] , with the two enzymes being homologous to the two modern synthetase classes. Considering all three reading frames, we found that over 16% of the (X, Y) pairs have homologous pairs (X′, Y′) that can be encoded in a fully overlapping manner, with a level of X/X′ and Y/Y′ homology corresponding to Blast E-values of 10 −10 or less and a match length of at least 85% of the total sequence length. Given the level of success and the generality of our algorithm, we also designed 200 triple genes, with three proteins encoded by the same DNA segment using both strands and three different reading frames.	./cache/cord-002758-d86hnox1.txt	./txt/cord-002758-d86hnox1.txt