ArticleNucleic acids research2011
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited.Bioinformatics (Oxford, England) · 2021Article
- Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences.Algorithms for molecular biology : AMB · 2020Article
- Unrealistic phylogenetic trees may improve phylogenetic footprinting.Bioinformatics (Oxford, England) · 2017Article
- Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.BMC bioinformatics · 2016Article
- Computational approaches to study the effects of small genomic variations.Journal of molecular modeling · 2015Review
- GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.Nucleic acids research · 2015Article
- TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.Nucleic acids research · 2015Article
- YOC, A new strategy for pairwise alignment of collinear genomes.BMC bioinformatics · 2015Article
- IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.Evolutionary bioinformatics online · 2015Review
- The Genome 10K Project: a way forward.Annual review of animal biosciences · 2015Review
- Alignathon: a competitive assessment of whole-genome alignment methods.Genome research · 2014Article
- Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.PLoS computational biology · 2014Article
- PSAR-align: improving multiple sequence alignment using probabilistic sampling.Bioinformatics (Oxford, England) · 2014Article
- Evaluating the accuracy and efficiency of multiple sequence alignment methods.Evolutionary bioinformatics online · 2014Article
- Accuracy estimation and parameter advising for protein multiple sequence alignment.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
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2 authors.
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Abstract
Multiple sequence alignment, which is of fundamental importance for comparative genomics, is a difficult problem and error-prone. Therefore, it is essential to measure the reliability of the alignments and incorporate it into downstream analyses. We propose a new probabilistic sampling-based alignment reliability (PSAR) score. Instead of relying on heuristic assumptions, such as the correlation between alignment quality and guide tree uncertainty in progressive alignment methods, we directly generate suboptimal alignments from an input multiple sequence alignment by a probabilistic sampling method, and compute the agreement of the input alignment with the suboptimal alignments as the alignment reliability score. We construct the suboptimal alignments by an approximate method that is based on pairwise comparisons between each single sequence and the sub-alignment of the input alignment where the chosen sequence is left out. By using simulation-based benchmarks, we find that our approach is superior to existing ones, supporting that the suboptimal alignments are highly informative source for assessing alignment reliability. We apply the PSAR method to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study.
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