A bio-inspired approach for multi-word expression extraction
COLING-ACL '06 Proceedings of the COLING/ACL on Main conference poster sessions
A Faster Algorithm for RNA Co-folding
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Fast RNA Structure Alignment for Crossing Input Structures
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Sparse RNA Folding: Time and Space Efficient Algorithms
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Efficient alignment of RNAs with pseudoknots using sequence alignment constraints
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on applications of signal procesing techniques to bioinformatics, genomics, and proteomics
Constraint-Based Strategy for Pairwise RNA Secondary Structure Prediction
EPIA '09 Proceedings of the 14th Portuguese Conference on Artificial Intelligence: Progress in Artificial Intelligence
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Fast RNA structure alignment for crossing input structures
Journal of Discrete Algorithms
Sparse RNA folding: Time and space efficient algorithms
Journal of Discrete Algorithms
Fast and accurate structural RNA alignment by progressive lagrangian optimization
CompLife'05 Proceedings of the First international conference on Computational Life Sciences
NcRNA homology search using Hamming distance seeds
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Exact pattern matching for RNA structure ensembles
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on foldalign and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as well as for substitution matrices similar to RIBOSUM. The new foldalign implementation is tested on a dataset where the ncRNAs and eleRNAs have sequence similarity foldalign is substantially faster. The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability: The program is available online at http://foldalign.kvl.dk/ Contact: gorodkin@bioinf.kvl.dk