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compgenomics:modul2 [2025/05/16 08:27] – [Analysis] felixcompgenomics:modul2 [2025/05/17 12:54] (current) – felix
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-Genes in two species that originated from the same ancestral gene in the last common ancestor of the species are good candidates for being 'corresponding' genes (orthologs)+**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 'corresponding' genes (orthologs)
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-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  the distribution of 235 potential PCDs across all eukaryotic datasets available in the RefSeq database.+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 ===
  
-  - Open a visualizaiton of the results generated by Tran et al. (2025) using [[https://ebersberger-46-155.biologie.uni-frankfurt.de/phyloppcd/|this interactive web-viewer]] +The task at hand is to find out which genes "correspond" to each other in different species and should be displayed in the same row.   
 + 
 +Have another look at the assumptions at the top of the page. Our best bet to find "corresponding" genes between species is to identify orthologs. In practice, this means finding genes in two species that are mutually most similar to each other. 
 + 
 +Finding genes with significantly similar sequences is typically done with a BLAST search. To identify orthologs, we will perform a "reciprocal best hit search". As an example, we will use the GH45 type cellulase of //Rhizoctonia solani// ([[https://www.ncbi.nlm.nih.gov/protein/XP_043186466.1?report=genbank&log\$=prottop&blast_rank=1&RID=2A0JJUND016|XP_043186466.1]]). 
 + 
 +  - Open [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome|NCBI BLAST]] 
 +  - Start a search with the following parameters: 
 +    - Paste the sequence accession number into the search field: <wrap tip>XP_043186466.1</wrap> 
 +    - Select database: <wrap tip>Reference proteins (refseq_protein)</wrap> 
 +    - Select target species: <wrap tip>//Bradysia coprophila//</wrap> 
 +  - Extract the accession number of the best hit 
 +  - Perform reverse BLAST serach in //Rhizoctonia solani// 
 + 
 +=== Task 2: Exploration === 
 + 
 +  - Open a visualizaiton of the results generated using [[https://ebersberger-46-155.biologie.uni-frankfurt.de/phyloppcd/|this interactive web-viewer]] 
 +  - <wrap important>Alternatively:</wrap> start PhyloProfile locally and input the data deposited at: ''https://applbio.biologie.uni-frankfurt.de/download/fDOG_pPCD/pPCD-PhylogeneticProfiles.tar.gz'' 
   - <wrap tip>Wait a moment </wrap> for the data to load. Once you were redirected to the "Main profile" page, select a taxonomic rank and click the red **PLOT** button   - <wrap tip>Wait a moment </wrap> for the data to load. Once you were redirected to the "Main profile" page, select a taxonomic rank and click the red **PLOT** button
   - Explore the "Main plot" on different taxonomic levels   - Explore the "Main plot" on different taxonomic levels
-  - Select the "Dimension reduction" plot from the top menu and explore the plot with "Phylum"-level labels +    - 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? 
-=== Task 2: Finding corresponding genes ===+    - What patterns can you observe in the plot and how do you interpret them?
  
-After having explored the results, let's find out how they were generated. Have another look at the assumptions at the top of the page. +=== Summary and Disussion ===
  
 +  * Record your observations and questions
 +  * Discuss with the group
  
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