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Day 4: Pan and core genome plots

Pan and core genome plots

Pan and core genome plots are graphs that display to what extent gene familes are conserved within a set of genomes. Conservation is evaluated by first BLASTing the proteomes of the genomes againt each other. This is done in a certain order, in that for every proteome, it performs a BLAST search against all previous proteomes. The result is a set of numbers specific for that time point that represents the proteome in the order of the input list, showing:

  • Number of new genes
  • Number of new families
  • Size of core genome
  • Size of pan genome
Two genes are considered to belong to the same gene family if the two are more than 50% identical over more than 50% of the length of the longest of the two genes.

We have prepared a script which produces such a pan- and coregenome plot, provided a list of proteomes.The result is a set of numbers specific for that time point that represents the proteome in the order of the input list. The script will accept a number of proteomes (pr1, pr2, .. prN) and perform a BLAST search of each proteome against all the previous:
  • pr2 against pr1
  • pr3 against pr1+pr2
  • pr4 against pr1+pr2+pr3
  • ...
  • prN against pr1+pr2+pr3 ... pr[N-1]
After these searches, the program will derive the number of core and pan proteins for each proteome. The output list will the be redirected into an R-scriptwhich plots all the core/pan values as a function of the proteome number. Just like the BLAST matrix script you tried last week, this script will cache all the BLAST results. In the event you change the order of the input proteins, all BLAST searches must be carried out again.  However, since you last week did a blast matrix, all of these results are still stored, so changing the order should not be a problem this time.

  1. First, log in and create a directory for this work. You will also need X to look at the results. See the previous exercise for how to do this. 
    # log in to the computers again, then
    ssh -Y sbiology
    umask 022
    setenv MAKEFILES /home/people/pfh/bin/Makefile
  2. Create a directory where this work will be done.
    # Ensure you are in the right place
    cd ~/
    mkdir coregenome
    cd coregenome
  3. Create configuration file for this program
    # create config file
    sh ~karinl/scripts/core/coregenome.sh ../data/prodigal > pancoregenomelist.txt
  4. Look at this file using nedit (remember, you need to have X activated!)

    The order the organisms are listed in in the file decides the order of the organisms in the plot. The field on the left is the name of the organism, while the protein file for this organism is listed on the right.
    # look at, and maybe edit using nedit
    nedit pancoregenomelist.txt

    Save the file.

  5. Run the pan coregenome plot program.

    # run the program.
    perl ~pfh/scripts/coregenome/coregenome pancoregenomelist.txt > pancoregenomeplot.ps

  6. Examine the plot:
    # View the plot
    gv pancoregenomeplot.ps
    Look at the plot. Can you tell how many gene families, approximately, your genomes have in common? How many gene families are there in total for your genomes?