INSA - TP bioinformatique



Exercise 5: Database against database BLAST searches


Objective: compare the proteomes of Mycoplasma genitalium and Mycoplasma pneumoniae.
 

Step 1: Install BLAST on your local computer. BLAST executables are available at ftp://ftp.ncbi.nih.gov/blast/ (or HERE ). Carefully read the instructions in the BLAST distribution to install all necessary files and executables in your environment.

  • Create a directory named blast, and then de-compress and de-tar the BLAST archive in this directory.
  • Move BLAST executables (blastall and formatdb) in your bin directory.
  • Create in your home directory a file named .ncbirc. This file must contain the following lines (replace /home/duret/blast/ by the path to your own blast directory):
  • Define the following environment variables:

    set BLASTDB=/home/duret/blast/db/ (default repertory for BLAST databases)

    set BLASTMAT=/home/duret/blast/matrix/ (repertory containing substitution matrices)

    More help.

    Step 2: For each species (Mycoplasma genitalium, Mycoplasma pneumoniae), select all protein entries from SwissProt-TrEMBL using WWW-Query at PBIL, and then extract sequences in FASTA format.

    How many proteins are encoded by Mycoplasma genitalium and by Mycoplasma pneumoniae genomes ?

  • Step 2.1
  • Step 2.2

  • Step 3: Prepare a BLAST database with Mycoplasma pneumoniae proteins, and then BLAST (blastp) Mycoplasma genitalium proteins against this database.

    
    
    

    How many Mycoplasma genitalium proteins have at least one homologue in Mycoplasma pneumoniae ?