ArticleJournal of computational biology : a journal of computational molecular cell biology2009
Exact calculation of distributions on integers, with application to sequence alignment.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner.Genome biology · 2025Article
- RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.BMC bioinformatics · 2020Article
- Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.BMC bioinformatics · 2018Article
- Efficient calculation of exact probability distributions of integer features on RNA secondary structures.BMC genomics · 2014Article
- A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).Journal of computational biology : a journal of computational molecular cell biology · 2012Review
- RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences.Bioinformatics (Oxford, England) · 2011Article
- Improving the accuracy of predicting secondary structure for aligned RNA sequences.Nucleic acids research · 2011Article
- Parameters for accurate genome alignment.BMC bioinformatics · 2010Article
- Error statistics of hidden Markov model and hidden Boltzmann model results.BMC bioinformatics · 2009Article
- Fewer permutations, more accurate P-values.Bioinformatics (Oxford, England) · 2009Article
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2 authors.
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Abstract
Computational biology is replete with high-dimensional discrete prediction and inference problems. Dynamic programming recursions can be applied to several of the most important of these, including sequence alignment, RNA secondary-structure prediction, phylogenetic inference, and motif finding. In these problems, attention is frequently focused on some scalar quantity of interest, a score, such as an alignment score or the free energy of an RNA secondary structure. In many cases, score is naturally defined on integers, such as a count of the number of pairing differences between two sequence alignments, or else an integer score has been adopted for computational reasons, such as in the test of significance of motif scores. The probability distribution of the score under an appropriate probabilistic model is of interest, such as in tests of significance of motif scores, or in calculation of Bayesian confidence limits around an alignment. Here we present three algorithms for calculating the exact distribution of a score of this type; then, in the context of pairwise local sequence alignments, we apply the approach so as to find the alignment score distribution and Bayesian confidence limits.
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