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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| compgenomics:modul2 [2025/05/16 08:21] – felix | compgenomics:modul2 [2025/05/17 12:54] (current) – felix | ||
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| <WRAP round tip 500px center> | <WRAP round tip 500px center> | ||
| - | Genes in two species that originated from the same ancestral gene in the last common ancestor of the species are good candidates for being ' | + | **Assumption 1:** Genes in two species that originated from the same ancestral gene in the last common ancestor of the species are good candidates for being ' |
| </ | </ | ||
| <WRAP round tip 500px center> | <WRAP round tip 500px center> | ||
| - | Orthologs are genes in two species that are mutually most similar to each other | + | **Assumption 2:** Orthologs are genes in two species that are mutually most similar to each other |
| </ | </ | ||
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| It was thought for a long time that PCDs are only produced by fungi and certain bacteria, but in recent years, evidence has accumulated that some invertebrate animals may be able to degrade plant cell walls as well. | It was thought for a long time that PCDs are only produced by fungi and certain bacteria, but in recent years, evidence has accumulated that some invertebrate animals may be able to degrade plant cell walls as well. | ||
| - | To find out how widespread the ability to degrade plant cell wall, really is Tran et al. (2025) traced | + | To find out how widespread the ability to degrade plant cell wall, really is we trace the distribution of 235 potential PCDs across all eukaryotic datasets available in the RefSeq database. |
| - | === Task 1: Exploration | + | === Task 1: Finding corresponding genes === |
| - | - Explore the results generated by Tran et al. (2025) using [[https:// | + | The task at hand is to find out which genes "correspond" |
| - | - <wrap tip>Wait a moment for the data to load. Once you were redirected to the "Main profile" | + | |
| + | Have another look at the assumptions at the top of the page. Our best bet to find " | ||
| + | |||
| + | Finding genes with significantly similar sequences is typically done with a BLAST search. To identify orthologs, we will perform a " | ||
| + | |||
| + | - Open [[https:// | ||
| + | - Start a search with the following parameters: | ||
| + | - Paste the sequence accession number into the search field: <wrap tip> | ||
| + | - Select database: <wrap tip> | ||
| + | - Select target species: <wrap tip>// | ||
| + | - Extract the accession number of the best hit | ||
| + | - Perform reverse BLAST serach in // | ||
| + | |||
| + | === Task 2: Exploration === | ||
| + | |||
| + | - Open a visualizaiton of the results generated using [[https:// | ||
| + | - <wrap important> | ||
| + | - <wrap tip>Wait a moment </ | ||
| + | - Explore the "Main plot" on different taxonomic levels | ||
| + | - You can draw selection boxes on the overview plot and generate a more detailed plot of the selected section | ||
| + | - Which information is displayed in the rows, which in the columns? | ||
| + | - What patterns can you observe in the plot and how do you interpret them? | ||
| + | |||
| + | === Summary and Disussion === | ||
| + | |||
| + | * Record your observations and questions | ||
| + | * Discuss with the group | ||
| ---- | ---- | ||
| [[: | [[: | ||