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compgenomics:modul4 [2025/05/16 11:01] – [Analysis] felixcompgenomics:modul4 [2025/05/16 11:12] (current) – [From gene presence to function] felix
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 <WRAP round tip 500px center> <WRAP round tip 500px center>
-Information about gene activity can be extracted from the sequence+**Assumption:** Information about gene activity can be extracted from the sequence
 </WRAP> </WRAP>
  
 ==== Analysis ==== ==== Analysis ====
 +
 +The functional analysis of a protein sequence typically involves the annotation of features that are directly or indirectly related to the activity of the protein. Examples include structural protein domains, regions of conserved sequence, signal peptides and transmembrane domains, and low-complexity regions. Alterations in protein feature architectures have been associated with changes in protein activity. Therefore, the comparison of features can help to find out whether orthologs have adapted a different molecular activity in the course of their evolution.
  
 === Task 1: The CE8 pectinase === === Task 1: The CE8 pectinase ===
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   - Click on the corresponding dot and display the detailed plot   - Click on the corresponding dot and display the detailed plot
   - Select XP_037045633.1 and click on 'show domain architecture'   - Select XP_037045633.1 and click on 'show domain architecture'
-  - Which domains do you find annotated?+  - PhyloProfile will show you a comparison between the feature architecture of the CE8_QRW20161.1 ortholog in the fungus //Rhizoctonia solani// and the one in the invertebrate //Bradysia coprophila// 
 +  - Which domains do you find annotated in the fungus, which ones in the invertebrate? 
 +  - Which impact do you expect this observation to have on the pectinase-activity of the gene?
  
  
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   - Have a look at the available information about the [[https://www.ebi.ac.uk/interpro/entry/pfam/PF00295/|Glyco_hydro_28 domain]]   - Have a look at the available information about the [[https://www.ebi.ac.uk/interpro/entry/pfam/PF00295/|Glyco_hydro_28 domain]]
   - Now, find the domain plot for the ortholog in the invertebrate //Bradysia coprophila//   - Now, find the domain plot for the ortholog in the invertebrate //Bradysia coprophila//
-  - What differences do you observe?+  - What do you observe?