Linear time algorithms for NP-hard problems restricted to partial k-trees
Discrete Applied Mathematics
On the complexity of finding iso- and other morphisms for partial k-trees
Discrete Mathematics - Topological, algebraical and combinatorial structures; Froli´k's memorial volume
Tree adjoining grammars for RNA structure prediction
Theoretical Computer Science - Special issue: Genome informatics
Faster genome annotation of non-coding RNA families without loss of accuracy
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
FastR: Fast Database Search Tool for Non-Coding RNA
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Profiling and searching for RNA pseudoknot structures in genomes
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Graph algorithms for biological systems analysis
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Treewidth computations I. Upper bounds
Information and Computation
RNApasta: a tool for analysis of RNA structural alignments
International Journal of Bioinformatics Research and Applications
Rapid ab initio RNA folding including pseudoknots via graph tree decomposition
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Efficient parameterized algorithm for biopolymer structure-sequence alignment
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Finding good decompositions for dynamic programming on dense graphs
IPEC'11 Proceedings of the 6th international conference on Parameterized and Exact Computation
Tree decompositions of graphs: Saving memory in dynamic programming
Discrete Optimization
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Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time 0(k^t N^2 ), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.