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AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data

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Title AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data
 
Creator Alsamman, Alsamman
 
Contributor El Allali, Achraf
Mokhtar, Morad M.
El-Shamaa, Khaled
Nassar, Ahmed E.
Mousa, Khaled H.
Kehel, Zakaria
 
Subject alignstatplot
 
Description Multiple sequence alignment (MSA) is essential for understanding genetic variations con trolling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, mak ing viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce “AlignStatPlot,” a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy ses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software.
 
Date 2024-02-13T19:23:20Z
2024-02-13T19:23:20Z
 
Type Journal Article
 
Identifier https://mel.cgiar.org/reporting/download/hash/3144c74a38ebfec3a1babe4af315aac7
Alsamman Alsamman, Achraf El Allali, Morad M. Mokhtar, Khaled El-Shamaa, Ahmed E. Nassar, Khaled H. Mousa, Zakaria Kehel. (20/9/2023). AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data. PLoS ONE, 18 (9).
https://hdl.handle.net/20.500.11766/69172
Open access
 
Language en
 
Rights CC-BY-4.0
 
Format PDF
 
Publisher Public Library of Science
 
Source PLoS ONE;18,(2023)