Exercise 2: Search for homologues in sequence databases

Objective: retrieve homologues of human insulin in the genome of the nematode C. elegans.
 

Step 1: search for homologues of the human insulin protein  with BLAST at NCBI ( *** )

• standard protein-protein BLAST
• Database: nr
• Default parameters


Look at the results ( *** ) and the taxonomy report ( *** ). How many nematode insulin homologues did you find ? (NB: you can use the menu "Edit/Find" to search for nematode in the taxonomy report).
 

 
• standard protein-protein BLAST
• Database: nr
• Option:
  • Expect: 100
• Format:
  • Descriptions: 1000
  • Alignments: 1000
  • Layout: One window
• Other parameters: default
• Run BLAST, and then, in the Format window:
• Limit by entrez query: Caenorhabditis elegans

Look at the results. How many nematode insulin homologues did you find ?

Step 3: Now repeat the BLAST search with the same parameters, except the "Limit by entrez query" in the option section:

 
• standard protein-protein BLAST
• Database: nr
• Option:
  • Expect: 100
  • Limit by entrez query: Caenorhabditis elegans
• Format:
  • Descriptions: 1000
  • Alignments: 1000
  • Layout: One window
• Other parameters: default

Look at the results (  ***  ). How many nematode insulin homologues did you find ? How can you explain the difference with what you obtained in step 2 ?

Step 4: Now repeat the search with PSI-BLAST ( BLAST at NCBI ):

• PSI and PHI BLAST
• Database: nr
• Parameters: 1000 descriptions, 1000 alignments
• Layout: One window