id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-016261-jms7hrmp	Liu, Chunmei	Profiling and Searching for RNA Pseudoknot Structures in Genomes	2005		.txt	text/plain	4330	221	53	Profiling models based solely on sequence content such as Hidden Markov Model (HMM) [12] may miss structural homologies when directly used to search genomes for noncoding RNAs containing complex secondary structures. ERPIN searches genomes by sequentially looking for single stem loop motifs contained in the noncoding RNA gene, and reports a hit when significant alignment scores are observed for all the motifs at their corresponding locations. In this paper, we propose a new method to search for RNA pseudoknot structures using a model of multiple CMs. Unlike the model of Brown and Wilson, we use independent CM components to profile the interleaving stems in a pseudoknot. Finally, in order to test the ability of our program to cope with noncoding RNA genes with complex pseudoknot structures, we carried out an experiment where the complete DNA genomes of two bacteria were searched to find the locations of the tmRNA genes.	./cache/cord-016261-jms7hrmp.txt	./txt/cord-016261-jms7hrmp.txt