Post-Alignment Adjustment and Its Automation

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...

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Autor principal:	Xuhua Xia
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	sequence alignment automation sum-of-pairs score inconsistency position weight matrix PWM Genetics QH426-470
Acceso en línea:	https://doaj.org/article/555e85348f164acfb03912b94c76fd09
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spelling	oai:doaj.org-article:555e85348f164acfb03912b94c76fd092021-11-25T17:42:16ZPost-Alignment Adjustment and Its Automation10.3390/genes121118092073-4425https://doaj.org/article/555e85348f164acfb03912b94c76fd092021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1809https://doaj.org/toc/2073-4425Multiple 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.Xuhua XiaMDPI AGarticlesequence alignmentautomationsum-of-pairs scoreinconsistencyposition weight matrixPWMGeneticsQH426-470ENGenes, Vol 12, Iss 1809, p 1809 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	sequence alignment automation sum-of-pairs score inconsistency position weight matrix PWM Genetics QH426-470
spellingShingle	sequence alignment automation sum-of-pairs score inconsistency position weight matrix PWM Genetics QH426-470 Xuhua Xia Post-Alignment Adjustment and Its Automation
description	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.
format	article
author	Xuhua Xia
author_facet	Xuhua Xia
author_sort	Xuhua Xia
title	Post-Alignment Adjustment and Its Automation
title_short	Post-Alignment Adjustment and Its Automation
title_full	Post-Alignment Adjustment and Its Automation
title_fullStr	Post-Alignment Adjustment and Its Automation
title_full_unstemmed	Post-Alignment Adjustment and Its Automation
title_sort	post-alignment adjustment and its automation
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/555e85348f164acfb03912b94c76fd09
work_keys_str_mv	AT xuhuaxia postalignmentadjustmentanditsautomation
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Post-Alignment Adjustment and Its Automation

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