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» Internal loops in RNA secondary structure prediction
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BMCBI
2008
123views more  BMCBI 2008»
14 years 9 months ago
Shape based indexing for faster search of RNA family databases
Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally ...
Stefan Janssen, Jens Reeder, Robert Giegerich
BMCBI
2011
14 years 1 months ago
RAG: An Update to the RNA-As-Graphs Resource
Background: In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structur...
Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tam...
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BMCBI
2006
142views more  BMCBI 2006»
14 years 9 months ago
RDMAS: a web server for RNA deleterious mutation analysis
Background: The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious...
Wenjie Shu, Xiaochen Bo, Rujia Liu, Dongsheng Zhao...
BMCBI
2010
175views more  BMCBI 2010»
14 years 9 months ago
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe
Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly ...
S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veerav...
BMCBI
2008
140views more  BMCBI 2008»
14 years 9 months ago
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
Background: Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations ...
Kazutaka Katoh, Hiroyuki Toh