AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data
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 look...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Public Library of Science
2024
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| Acceso en línea: | https://hdl.handle.net/10568/139335 |
| _version_ | 1855517899142201344 |
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| author | Alsamman, Alsamman M. El Allali, Achraf Mokhtar, Morad M. Al-Shamaa, Khaled Nassar, Ahmed E. Mousa, Khaled H. Kehel, Zakaria |
| author_browse | Al-Shamaa, Khaled Alsamman, Alsamman M. El Allali, Achraf Kehel, Zakaria Mokhtar, Morad M. Mousa, Khaled H. Nassar, Ahmed E. |
| author_facet | Alsamman, Alsamman M. El Allali, Achraf Mokhtar, Morad M. Al-Shamaa, Khaled Nassar, Ahmed E. Mousa, Khaled H. Kehel, Zakaria |
| author_sort | Alsamman, Alsamman M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| 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. |
| format | Journal Article |
| id | CGSpace139335 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1393352026-01-14T02:03:25Z AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data Alsamman, Alsamman M. El Allali, Achraf Mokhtar, Morad M. Al-Shamaa, Khaled Nassar, Ahmed E. Mousa, Khaled H. Kehel, Zakaria big data genetics stocks alignstatplot 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. 2024-02-13T19:38:00Z 2024-02-13T19:38:00Z Journal Article https://hdl.handle.net/10568/139335 en Open Access application/pdf Public Library of Science Alsamman M. Alsamman, Achraf El Allali, Morad M. Mokhtar, Khaled Al-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). |
| spellingShingle | big data genetics stocks alignstatplot Alsamman, Alsamman M. El Allali, Achraf Mokhtar, Morad M. Al-Shamaa, Khaled Nassar, Ahmed E. Mousa, Khaled H. Kehel, Zakaria AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| title | AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| title_full | AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| title_fullStr | AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| title_full_unstemmed | AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| title_short | AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| title_sort | alignstatplot an r package and online tool for robust sequence alignment statistics and innovative visualization of big data |
| topic | big data genetics stocks alignstatplot |
| url | https://hdl.handle.net/10568/139335 |
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