Prediction of Consensus RNA Secondary Structures Including Pseudoknots
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast detection of common sequence structure patterns in RNAs
Journal of Discrete Algorithms
A Faster Algorithm for RNA Co-folding
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Predicting RNA secondary structure based on the class information and Hopfield network
Computers in Biology and Medicine
Simultaneous Alignment and Folding of Protein Sequences
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular 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
Lock-free parallel dynamic programming
Journal of Parallel and Distributed Computing
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
Structural alignment of two RNA sequences with lagrangian relaxation
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
Exact pattern matching for RNA structure ensembles
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Constructing structural alignment of RNA sequences by detecting and assessing conserved stems
LSMS'07 Proceedings of the 2007 international conference on Life System Modeling and Simulation
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
| Hi-index | 3.84 |
Motivation: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be constructed only when the shared structural features are taken into account. Since multiple alignments are used as input for many subsequent methods of data analysis, structure-based alignments are an indispensable necessity in RNA bioinformatics. Results: We present here a method to compute pairwise and progressive multiple alignments from the direct comparison of base pairing probability matrices. Instead of attempting to solve the folding and the alignment problem simultaneously as in the classical Sankoff's algorithm, we use McCaskill's approach to compute base pairing probability matrices which effectively incorporate the information on the energetics of each sequences. A novel, simplified variant of Sankoff's algorithms can then be employed to extract the maximum-weight common secondary structure and an associated alignment. Availability: The programs pmcomp and pmmulti described in this contribution are implemented in Perl and can be downloaded together with the example datasets from http://www.tbi.univie.ac.at/RNA/PMcomp/. A web server is available at http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl