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» A Computational Model for RNA Multiple Structural Alignment.
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HPCC
2005
Springer
14 years 2 months ago
Fast Sparse Matrix-Vector Multiplication by Exploiting Variable Block Structure
Abstract. We improve the performance of sparse matrix-vector multiplication (SpMV) on modern cache-based superscalar machines when the matrix structure consists of multiple, irregu...
Richard W. Vuduc, Hyun-Jin Moon
NAR
2007
153views more  NAR 2007»
13 years 8 months ago
PROMALS web server for accurate multiple protein sequence alignments
Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs mu...
Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grish...
TCBB
2011
13 years 4 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...
BIBE
2005
IEEE
121views Bioinformatics» more  BIBE 2005»
14 years 2 months ago
RNA Pseudoknot Prediction Using Term Rewriting
RNA plays a critical role in mediating every step of cellular information transfer from genes to functional proteins. Pseudoknots are widely occurring structural motifs found in a...
Xuezheng Fu, Hao Wang, William L. Harrison, Robert...
WABI
2007
Springer
133views Bioinformatics» more  WABI 2007»
14 years 3 months ago
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound
Predicting the secondary structure of an RNA sequence is an important problem in structural bioinformatics. The general RNA folding problem, where the sequence to be folded may con...
Chunmei Liu, Yinglei Song, Louis W. Shapiro