meta data for this page
  •  

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
compgenomics:modul2 [2025/05/17 09:50] – [Analysis] felixcompgenomics:modul2 [2025/09/23 13:53] (current) – felix
Line 15: Line 15:
 </WRAP> </WRAP>
  
-==== Analysis ====+===== Analysis =====
  
 In this course, we will follow the steps of a [[https://www.biorxiv.org/content/10.1101/2024.10.16.618745v2|comparative genomics analysis of plant cell wall degrading enzymes]] (PCDs). Plant cell walls are made up of cellulose and hemi-cellulose, making them two of the most common organic molecules on Earth and key components of the carbon cycle. In this course, we will follow the steps of a [[https://www.biorxiv.org/content/10.1101/2024.10.16.618745v2|comparative genomics analysis of plant cell wall degrading enzymes]] (PCDs). Plant cell walls are made up of cellulose and hemi-cellulose, making them two of the most common organic molecules on Earth and key components of the carbon cycle.
Line 23: Line 23:
 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. 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: Finding corresponding genes ===+==== Task 1: Finding corresponding genes ====
  
 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.   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.  
Line 39: Line 39:
   - Perform reverse BLAST serach in //Rhizoctonia solani//   - Perform reverse BLAST serach in //Rhizoctonia solani//
  
-=== Task 2: Exploration ===+==== Task 2: Exploration ====
  
-  - Open a visualizaiton of the results generated using [[https://ebersberger-46-155.biologie.uni-frankfurt.de/phyloppcd/|this interactive web-viewer]] +=== Option 1: Webviewer (if currently online) === 
 + 
 +  - Open the visualizaiton of the results using [[https://ebersberger-46-155.biologie.uni-frankfurt.de/phyloppcd/|this interactive web-viewer]] 
 + 
 +=== Route 2: Local PhyloProfile installation === 
 + 
 +  - Install Miniconda<WRAP> 
 +<code> 
 +mkdir -p ~/miniconda3 
 +wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh 
 +bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 
 +rm ~/miniconda3/miniconda.sh 
 +</code></WRAP> 
 +  - Install Conplex (our local software management system)<WRAP> 
 +<code> 
 +echo 'CONPLEX_ENVS_FILE=/home/worker/data/conplex/envs.tsv' >> ~/.bashrc 
 +echo 'alias conplex="source /home/worker/bin/conplex.sh"' >> ~/.bashrc 
 +source ~/.bashrc 
 +</code></WRAP> 
 +  -  Download and unpack the input data<WRAP> 
 +<code> 
 +wget https://applbio.biologie.uni-frankfurt.de/download/fDOG_pPCD/pPCD-PhylogeneticProfiles.tar.gz 
 +tar -zxvf pPCD-PhylogeneticProfiles.tar.gz 
 +</code></WRAP> 
 +  - Start Phyloprofile<WRAP> 
 +<code> 
 +conplex load phyloprofile 
 +</code></WRAP> 
 +  - Upload the file you downloaded to PhyloProfile
   - <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
Line 47: Line 75:
     - Which information is displayed in the rows, which in the columns?     - 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?     - What patterns can you observe in the plot and how do you interpret them?
-  - Select the "Dimension reduction" plot from the top menu and explore the plot with "Phylum"-level labels 
  
 === Summary and Disussion === === Summary and Disussion ===