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Article

Post-Alignment Adjustment and Its Automation

by 1,2
1
Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada
2
Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
Academic Editor: Sujoy Ghosh
Genes 2021, 12(11), 1809; https://doi.org/10.3390/genes12111809
Received: 28 October 2021 / Revised: 13 November 2021 / Accepted: 16 November 2021 / Published: 18 November 2021
Multiple sequence alignment (MSA) is the basis for almost all sequence comparison and molecular phylogenetic inferences. Large-scale genomic analyses are typically associated with automated progressive MSA without subsequent manual adjustment, which itself is often error-prone because of the lack of a consistent and explicit criterion. Here, I outlined several commonly encountered alignment errors that cannot be avoided by progressive MSA for nucleotide, amino acid, and codon sequences. Methods that could be automated to fix such alignment errors were then presented. I emphasized the utility of position weight matrix as a new tool for MSA refinement and illustrated its usage by refining the MSA of nucleotide and amino acid sequences. The main advantages of the position weight matrix approach include (1) its use of information from all sequences, in contrast to other commonly used methods based on pairwise alignment scores and inconsistency measures, and (2) its speedy computation, making it suitable for a large number of long viral genomic sequences. View Full-Text
Keywords: sequence alignment; automation; sum-of-pairs score; inconsistency; position weight matrix; PWM; codon-based alignment; phylogenetics sequence alignment; automation; sum-of-pairs score; inconsistency; position weight matrix; PWM; codon-based alignment; phylogenetics
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MDPI and ACS Style

Xia, X. Post-Alignment Adjustment and Its Automation. Genes 2021, 12, 1809. https://doi.org/10.3390/genes12111809

AMA Style

Xia X. Post-Alignment Adjustment and Its Automation. Genes. 2021; 12(11):1809. https://doi.org/10.3390/genes12111809

Chicago/Turabian Style

Xia, Xuhua. 2021. "Post-Alignment Adjustment and Its Automation" Genes 12, no. 11: 1809. https://doi.org/10.3390/genes12111809

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