TP bioinformatique

Exercise 7: Database against database BLAST searches

1 - Comparison of 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/. Carefully read the instructions in the BLAST distribution to install all necessary files and executables in your environment.

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

2 - Comparison of the proteomes of Mycoplasma genitalium, Mycoplasma pneumoniae and Mycoplasma penetrans

Use BLASTCLUST to identify families of homologous proteins present in the three species and sharing at least 50% identity over at least 70% of their length.
How many protein families have at least one homologue in each species ?
How many proteins are specific to Mycoplasma pneumoniae ?
How many proteins are specific to Mycoplasma genitalium ?
How many proteins are specific to Mycoplasma penetrans ?

Try to answer the same questions using the HOGENOM database and the Cross-Taxa tool.

Help!!