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Abstract: Many classes of functional RNA molcules 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. Sankoff's algorithm can be used to construct such structure-based alignments of RNA sequences in polynomial time. Here we extend the approach to a probabilistic one by explicitly computing the partition function of all pairwisely... (Update)
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0.7: A Novel Approach to Local Reliability of Sequence Alignments - Schlosshauer, Ohlsson (2001) (Correct)
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BibTeX entry: (Update)
@misc{ hofacker-partition,
author = "Ivo Hofacker",
title = "The Partition Function Variant of Sankoff's Algorithm",
url = "citeseer.ist.psu.edu/699311.html" }
Citations (may not include all citations):92 Fast folding and comparison of RNA secondary structures - Hofacker, Fontana et al. - 1994
78 An improved algorithm for matching biological sequences (context) - Gotoh - 1982
71 The equilibrium partition function and base pair binding pro.. (context) - McCaskill - 1990
33 Expanded sequence dependence of thermodynamic parameters pro.. (context) - Mathews, Sabina et al. - 1999
26 The protein threading problem with sequence amino acid inter.. - Lathrop - 1994
9 Algorithm independent properties of RNA structure prediction (context) - Tacker, Stadler et al. - 1996
8 Finding the most significant common sequence and structure m.. (context) - Gorodkin, Heyer et al. - 1997
7 Compilation of tRNA sequences and sequences of tRNA genes (context) - Sprinzl, Horn et al. - 1998
6 A sequence similarity search algorithm based on a probabilis.. (context) - Bucher, Ho - 1996
5 Noncoding RNA gene detection using comparative sequence anal.. (context) - Rivas, Eddy - 2001
5 Vienna RNA secondary structure server - Hofacker - 2003
4 A reliable sequence alignment method based on probabilities .. (context) - Miyazawa - 1994
4 Dynalign: An algorithm for finding secondary structures comm.. (context) - Mathews, Turner - 2002
3 Stochastic pairwise alignments (context) - Muckstein, Hofacker et al. - 2002
2 Finite-temperature sequence alignment - Kschischo, Lassig - 2000
2 A statistical sampling algorithm for RNA secondary structure.. (context) - Ding, Lawrence - 2003
2 Alignment of rna base pairing probability matrices (context) - Hofacker, Berhart et al. - 2003
2 Statistical significance of probabilistic sequence alignment.. (context) - Yu, Hwa - 2001
1 Statistical prediction of single-stranded regions in RNA sec.. (context) - Ding, Lawrence - 2001
1 Computational chemistry with RNA secondary structures - Flamm, Hofacker et al. - 2003
1 ee: A novel method for multiple sequence alignments (context) - Notredame, Higgins et al. - 2000
Documents on the same site (http://www.tbi.univie.ac.at/~ivo/publications.html): More
RNA in Silico - The Computational Biology of RNA.. - Flamm, Hofacker, Stadler (1999) (Correct)
RNA Secondary Structures: A Tractable Model of Biopolymer Folding - Hofacker (1998) (Correct)
Automatic Detection of Conserved Base Pairing Patterns in.. - Hofacker, Stadler (1998) (Correct)
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