ArticleBioinformatics (Oxford, England)2022
On the reliability and the limits of inference of amino acid sequence alignments.
Article in Bioinformatics (Oxford, England), 2022. 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.
- Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.Protein science : a publication of the Protein Society · 2025Article
- Gene-level alignment of single-cell trajectories.Nature methods · 2025Article
- Comparative Analyses of Bacteriophage Genomes.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Odor-evoked transcriptomics of Aedes aegypti mosquitoes.PloS one · 2023Article
- Bridging the gaps in statistical models of protein alignment.Bioinformatics (Oxford, England) · 2022Article
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8 authors.
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Abstract
motivationAlignments are correspondences between sequences. How reliable are alignments of amino acid sequences of proteins, and what inferences about protein relationships can be drawn? Using techniques not previously applied to these questions, by weighting every possible sequence alignment by its posterior probability we derive a formal mathematical expectation, and develop an efficient algorithm for computation of the distance between alternative alignments allowing quantitative comparisons of sequence-based alignments with corresponding reference structure alignments.
resultsBy analyzing the sequences and structures of 1 million protein domain pairs, we report the variation of the expected distance between sequence-based and structure-based alignments, as a function of (Markov time of) sequence divergence. Our results clearly demarcate the 'daylight', 'twilight' and 'midnight' zones for interpreting residue-residue correspondences from sequence information alone. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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