Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Predicting RNA secondary structure based on the class information and Hopfield network
Computers in Biology and Medicine
Lifting Prediction to Alignment of RNA Pseudoknots
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Conserved secondary structure prediction for similar highly group of related RNA sequences
CCDC'09 Proceedings of the 21st annual international conference on Chinese control and decision conference
PMFastR: a new approach to multiple RNA structure alignment
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes
Theoretical Computer Science
A Memory Efficient Method for Structure-Based RNA Multiple Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast and accurate structural RNA alignment by progressive lagrangian optimization
CompLife'05 Proceedings of the First international conference on Computational Life Sciences
Multiple structural RNA alignment with lagrangian relaxation
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Exact pattern matching for RNA structure ensembles
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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Motivation: Due to the importance of considering secondary structures in aligning functional RNAs, several pairwise sequence--structure alignment methods have been developed. They use extended alignment scores that evaluate secondary structure information in addition to sequence information. However, two problems for the multiple alignment step remain. First, how to combine pairwise sequence--structure alignments into a multiple alignment and second, how to generate secondary structure information for sequences whose explicit structural information is missing. Results: We describe a novel approach for multiple alignment of RNAs (MARNA) taking into consideration both the primary and the secondary structures. It is based on pairwise sequence--structure comparisons of RNAs. From these sequence--structure alignments, libraries of weighted alignment edges are generated. The weights reflect the sequential and structural conservation. For sequences whose secondary structures are missing, the libraries are generated by sampling low energy conformations. The libraries are then processed by the T-Coffee system, which is a consistency based multiple alignment method. Furthermore, we are able to extract a consensus-sequence and -structure from a multiple alignment. We have successfully tested MARNA on several datasets taken from the Rfam database. Availability: MARNA can be used online on our webpage www.bio.inf.uni-jena.de/Software/MARNA/index.html Contact: backofen@inf.uni-jena.de