id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-000822-iuglkdcp	Sperschneider, Jana	Predicting pseudoknotted structures across two RNA sequences	2012-12-01		.txt	text/plain	5494	386	61	One strong point of the DotKnot method for single sequence pseudoknot prediction (Sperschneider and Datta, 2010; Sperschneider et al., 2011) is that the set of possible H-type pseudoknot candidates (and secondary structure elements) is explicitly computed and thus readily available for further investigation. (3) Use significant pairs to calculate the set of conserved structure elements and pseudoknots for the two sequences that maximizes a combined free energy and similarity score. The key point of the DotKnot-PW approach is how to score the similarity of stems, secondary structure elements and H-type pseudoknot candidates derived from sequences Seq x and Seq y . The optimal structure element alignment, which preserves the interval ordering includes structure elements p 1 , p 4 , p 7 in the first sequence and p 1 , p 4 , p 6 in the second sequence pairwise prediction with highest combined free energy and similarity score is taken, DotKnot-PW has an improved average MCC of 0.81.	./cache/cord-000822-iuglkdcp.txt	./txt/cord-000822-iuglkdcp.txt