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BMCBI
2004
133views more  BMCBI 2004»
13 years 8 months ago
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Background: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily co...
Robin D. Dowell, Sean R. Eddy
CIBCB
2005
IEEE
13 years 10 months ago
A Transcriptional Approach to Gene Clustering
— We present an integrative method for clustering coregulated genes and elucidating their underlying regulatory mechanisms. We use multi-state partition functions and thermodynam...
Ilias Tagkopoulos
BMCBI
2010
155views more  BMCBI 2010»
13 years 6 months ago
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation
Background: Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products a...
Constantin Bannert, A. Welfle, C. aus dem Spring, ...
BMCBI
2004
229views more  BMCBI 2004»
13 years 8 months ago
Automatic annotation of protein motif function with Gene Ontology terms
Background: Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern search...
Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishna...
RECOMB
2005
Springer
14 years 9 months ago
RNA-RNA Interaction Prediction and Antisense RNA Target Search
Abstract. Recent studies demonstrating the existence of special non-coding "antisense" RNAs used in post-transcriptional gene regulation have received considerable attent...
Can Alkan, Emre Karakoç, Joseph H. Nadeau, ...