Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

Jakob H Havgaard; Elfar Torarinsson; Jan Gorodkin

doi:10.1371/journal.pcbi.0030193

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Open Access

Peer-reviewed

Research Article

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

Jakob H Havgaard,

Affiliation Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark
⨯
Elfar Torarinsson,

Affiliations Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark , Department of Natural Sciences, University of Copenhagen, Frederiksberg, Denmark
⨯
Jan Gorodkin

*To whom correspondence should be addressed. E-mail: gorodkin@genome.ku.dk

Affiliation Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark
⨯

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

Jakob H Havgaard,
Elfar Torarinsson,
Jan Gorodkin

Published: October 12, 2007
https://doi.org/10.1371/journal.pcbi.0030193

About the Authors

Jakob H Havgaard

Affiliation Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark

Elfar Torarinsson

Affiliations Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark , Department of Natural Sciences, University of Copenhagen, Frederiksberg, Denmark

Jan Gorodkin

*To whom correspondence should be addressed. E-mail: gorodkin@genome.ku.dk

Affiliation Division of Genetics and Bioinformatics, University of Copenhagen, Frederiksberg, Denmark

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

JHH and JG conceived and designed the experiments and wrote the paper. JHH and ET performed the experiments. All authors analyzed the data. JHH contributed reagents/materials/analysis tools.

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Sequence alignment
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RNA structure
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Nucleotides
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RNA alignment
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Nucleotide sequencing
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Transfer RNA
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Multiple alignment calculation
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RNA folding
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