A Faster Algorithm for RNA Co-folding
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Component-Based Modelling of RNA Structure Folding
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Constraint-Based Strategy for Pairwise RNA Secondary Structure Prediction
EPIA '09 Proceedings of the 14th Portuguese Conference on Artificial Intelligence: Progress in Artificial Intelligence
PMFastR: a new approach to multiple RNA structure alignment
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
A worst-case and practical speedup for the RNA co-folding problem using the four-Russians idea
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Sparse RNA folding: Time and space efficient algorithms
Journal of Discrete Algorithms
A Memory Efficient Method for Structure-Based RNA Multiple Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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: An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common structure between them. However, such a multiple alignment is hard to obtain even for few sequences with low sequence similarity without simultaneously folding and aligning them. Furthermore, it is of interest to conduct a multiple alignment of RNA sequence candidates found from searching as few as two genomic sequences. Results: Here, based on the PMcomp program, we present a global multiple alignment program, foldalignM, which performs especially well on few sequences with low sequence similarity, and is comparable in performance with state of the art programs in general. In addition, it can cluster sequences based on sequence and structure similarity and output a multiple alignment for each cluster. Furthermore, preliminary results with local datasets indicate that the program is useful for post processing foldalign pairwise scans. Availability: The program foldalignM is implemented in JAVA and is, along with some accompanying PERL scripts, available at http://foldalign.ku.dk/ Contact: gorodkin@genome.ku.dk