ArticleBioinformatics (Oxford, England)2020
How sequence alignment scores correspond to probability models.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Strategic Computational Design of siRNA Molecules Targeting Structural Genes of SARS-CoV-2.Applied biochemistry and biotechnology · 2026Article
- Pangenome-Informed Language Models for Synthetic Genome Sequence Generation.bioRxiv : the preprint server for biology · 2025Article
- Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.Bioinformatics (Oxford, England) · 2024Article
- nail: software for high-speed, high-sensitivity protein sequence annotation.bioRxiv : the preprint server for biology · 2024Article
- Short-read aligner performance in germline variant identification.Bioinformatics (Oxford, England) · 2023Review
- Topiary: Pruning the manual labor from ancestral sequence reconstruction.Protein science : a publication of the Protein Society · 2023Article
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Abstract
motivationSequence alignment remains fundamental in bioinformatics. Pair-wise alignment is traditionally based on ad hoc scores for substitutions, insertions and deletions, but can also be based on probability models (pair hidden Markov models: PHMMs). PHMMs enable us to: fit the parameters to each kind of data, calculate the reliability of alignment parts and measure sequence similarity integrated over possible alignments.
resultsThis study shows how multiple models correspond to one set of scores. Scores can be converted to probabilities by partition functions with a 'temperature' parameter: for any temperature, this corresponds to some PHMM. There is a special class of models with balanced length probability, i.e. no bias toward either longer or shorter alignments. The best way to score alignments and assess their significance depends on the aim: judging whether whole sequences are related versus finding related parts. This clarifies the statistical basis of sequence alignment. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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