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.
[NCBI] Data="/home/duret/blast/data/"
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)
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 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 ?