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» Problems on RNA Secondary Structure Prediction and Design
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JCC
2011
87views more  JCC 2011»
14 years 9 months ago
NUPACK: Analysis and design of nucleic acid systems
: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables...
Joseph N. Zadeh, Conrad Steenberg, Justin S. Bois,...
TCBB
2011
14 years 9 months ago
Semantics and Ambiguity of Stochastic RNA Family Models
Stochastic models such as hidden Markov models or stochastic context free grammars can fail to return the correct, maximum likelihood solution in the case of semantic ambiguity. T...
Robert Giegerich, Christian Höner zu Siederdi...
BMCBI
2007
156views more  BMCBI 2007»
15 years 1 months ago
Predictive modeling of plant messenger RNA polyadenylation sites
Background: One of the essential processing events during pre-mRNA maturation is the posttranscriptional addition of a polyadenine [poly(A)] tail. The 3'-end poly(A) track pr...
Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, ...
BMCBI
2008
134views more  BMCBI 2008»
15 years 2 months ago
Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites
Background: Utilization of alternative initiation sites for protein translation directed by non-AUG codons in mammalian mRNAs is observed with increasing frequency. Alternative in...
Jill L. Wegrzyn, Thomas M. Drudge, Faramarz Valafa...
GCB
2010
Springer
145views Biometrics» more  GCB 2010»
14 years 12 months ago
Shape-based Barrier Estimation for RNAs
: The ability of some RNA molecules to switch between different metastable conformations plays an important role in cellular processes. In order to identify such molecules and to p...
Sergiy Bogomolov, Martin Mann, Björn Voß...