ArticleBioinformatics (Oxford, England)2019
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Gene-level alignment of single-cell trajectories.Nature methods · 2025Article
- On the reliability and the limits of inference of amino acid sequence alignments.Bioinformatics (Oxford, England) · 2022Article
- Bridging the gaps in statistical models of protein alignment.Bioinformatics (Oxford, England) · 2022Article
- Three-dimensional Structure Databases of Biological Macromolecules.Methods in molecular biology (Clifton, N.J.) · 2022Article
- ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process.BMC bioinformatics · 2021Article
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3 authors.
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Abstract
The information criterion of minimum message length (MML) provides a powerful statistical framework for inductive reasoning from observed data. We apply MML to the problem of protein sequence comparison using finite state models with Dirichlet distributions. The resulting framework allows us to supersede the ad hoc cost functions commonly used in the field, by systematically addressing the problem of arbitrariness in alignment parameters, and the disconnect between substitution scores and gap costs. Furthermore, our framework enables the generation of marginal probability landscapes over all possible alignment hypotheses, with potential to facilitate the users to simultaneously rationalize and assess competing alignment relationships between protein sequences, beyond simply reporting a single (best) alignment. We demonstrate the performance of our program on benchmarks containing distantly related protein sequences. AVAILABILITY AND IMPLEMENTATION: The open-source program supporting this work is available from: http://lcb.infotech.monash.edu.au/seqmmligner. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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