Let's show Structural Variations
Genomes can be subject to Structural Variations (SVs): rearrangements of more than 50kb of a sequence of nucleotides. These variations can have various effects depending on where they take place in a genome (for example within a gene or a control region) and influence the phenotypes. Comparing these...
| Main Authors: | , , , |
|---|---|
| Format: | Poster |
| Language: | Inglés |
| Published: |
2023
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/130323 |
| _version_ | 1855527358503583744 |
|---|---|
| author | Durant, Éloi Conte, Matthieu Sabot, François Rouard, Mathieu |
| author_browse | Conte, Matthieu Durant, Éloi Rouard, Mathieu Sabot, François |
| author_facet | Durant, Éloi Conte, Matthieu Sabot, François Rouard, Mathieu |
| author_sort | Durant, Éloi |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Genomes can be subject to Structural Variations (SVs): rearrangements of more than 50kb of a sequence of nucleotides. These variations can have various effects depending on where they take place in a genome (for example within a gene or a control region) and influence the phenotypes. Comparing these SVs between genomes enables scientists to better understand the links between the rearrangements and their effects. However there are few tools that offer a visual exploration of these SVs, as most of them focus only on the sequences that are common between two genomes. We propose a visual representation of these SVs as a glyphs integrated within a matrix-like display, based on the divergences between to path / genomes within pangenome graphs. One genome acts as a reference coordinate system (the ‘pivot genome’), and all other genomes are then compared directly to it using the glyphs to highlight the differences. In order to create the most intuitive (therefore easiest to understand) glyphs for each type of SVs, we encourage the VIZBI community to answer a 1-minute survey and discover our proposed glyphs. |
| format | Poster |
| id | CGSpace130323 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| record_format | dspace |
| spelling | CGSpace1303232025-11-05T11:50:35Z Let's show Structural Variations Durant, Éloi Conte, Matthieu Sabot, François Rouard, Mathieu genomics genomes data graphics bioinformatics Genomes can be subject to Structural Variations (SVs): rearrangements of more than 50kb of a sequence of nucleotides. These variations can have various effects depending on where they take place in a genome (for example within a gene or a control region) and influence the phenotypes. Comparing these SVs between genomes enables scientists to better understand the links between the rearrangements and their effects. However there are few tools that offer a visual exploration of these SVs, as most of them focus only on the sequences that are common between two genomes. We propose a visual representation of these SVs as a glyphs integrated within a matrix-like display, based on the divergences between to path / genomes within pangenome graphs. One genome acts as a reference coordinate system (the ‘pivot genome’), and all other genomes are then compared directly to it using the glyphs to highlight the differences. In order to create the most intuitive (therefore easiest to understand) glyphs for each type of SVs, we encourage the VIZBI community to answer a 1-minute survey and discover our proposed glyphs. 2023-05 2023-05-11T08:12:23Z 2023-05-11T08:12:23Z Poster https://hdl.handle.net/10568/130323 en Open Access application/pdf Durant, E.; Conte, M.; Sabot, F.; Rouard, M. (2023) Let's show Structural Variations. 1 p. |
| spellingShingle | genomics genomes data graphics bioinformatics Durant, Éloi Conte, Matthieu Sabot, François Rouard, Mathieu Let's show Structural Variations |
| title | Let's show Structural Variations |
| title_full | Let's show Structural Variations |
| title_fullStr | Let's show Structural Variations |
| title_full_unstemmed | Let's show Structural Variations |
| title_short | Let's show Structural Variations |
| title_sort | let s show structural variations |
| topic | genomics genomes data graphics bioinformatics |
| url | https://hdl.handle.net/10568/130323 |
| work_keys_str_mv | AT duranteloi letsshowstructuralvariations AT contematthieu letsshowstructuralvariations AT sabotfrancois letsshowstructuralvariations AT rouardmathieu letsshowstructuralvariations |