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Partition function and base pairing probabilities of RNA heterodimers
 Algorithms Mol Biol
, 2006
"... Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inte ..."
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Cited by 68 (15 self)
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the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium
Using base pairing probabilities for MiRNA recognition
 In SYNASC ’08: Proceedings of the 2008 10th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing
, 2008
"... Abstract—We designed a new SVM for microRNA identification, whose novelty consist in the fact that many of its features incorporate the basepairing probabilities provided by McCaskill’s algorithm. Comparisons with other SVMs for microRNA identification prove that our SVM obtains competitive results ..."
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Cited by 1 (1 self)
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Abstract—We designed a new SVM for microRNA identification, whose novelty consist in the fact that many of its features incorporate the basepairing probabilities provided by McCaskill’s algorithm. Comparisons with other SVMs for microRNA identification prove that our SVM obtains competitive
Base Pairing Probabilities in a Complete HIV1 RNA
, 1996
"... We have calculated the base pair probability distribution for the secondary structure of a full length HIV1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By analyzing the full distribution of base pair probabilities instead of a restricted number of seconda ..."
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Cited by 2 (1 self)
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We have calculated the base pair probability distribution for the secondary structure of a full length HIV1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By analyzing the full distribution of base pair probabilities instead of a restricted number
Partition function and base pairing probabilities for RNARNA interaction prediction
 Bioinformatics
, 2009
"... The RNARNA interaction problems (RIP) deals with the energetically optimal structure of two RNA molecules that bind to each other. The standard model introduced by Alkan et al. (J. Comput. Biol. 13: 267282, 2006) allows secondary structures in both partners as well as additional base pairs between ..."
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Cited by 19 (8 self)
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programming approach is extended here by a fullfledged computation of the base pairing probabilities. The O(N6) time and O(N4) space algorithm is implemented in C (available from
Prediction Of Rna Base Pairing Probabilities Using Massively Parallel Computers
 J. Comp. Biol
, 1999
"... this document are those of the authors and should not be interpreted as necessarily representing the o#cial policies or endorsements, either expressed or implied, of Phillips Laboratory or the U.S. Government." Access to the CACR facility was provided by the California Institute of Technology i ..."
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Cited by 3 (2 self)
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this document are those of the authors and should not be interpreted as necessarily representing the o#cial policies or endorsements, either expressed or implied, of Phillips Laboratory or the U.S. Government." Access to the CACR facility was provided by the California Institute of Technology in the context of a collaboration with Paul E. Stolorz. Partial financial support by the Austrian 10
Pages 1–2 Local Base Pairing Probabilities in Large RNAs
, 2005
"... Summary: The genomewide search for and analysis of noncoding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a m ..."
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method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window.
APPLICATIONS NOTE Local RNA Base Pairing Probabilities in Large Sequences
"... Summary: The genomewide search for noncoding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a method for robust ..."
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for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window.
Secondary Structure of the 3'NonCoding Region of Flavivirus Genomes  Comparative Analysis of Base Pairing Probabilities
"... The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only welldefined secondary structure elements but also regions of high structural flexibility. Flaviviruses, many of which are im ..."
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Cited by 31 (8 self)
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The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only welldefined secondary structure elements but also regions of high structural flexibility. Flaviviruses, many of which
Results 1  10
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4,036,797