TP bioinformatique

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 (see exercise 1) with BLAST at NCBI ( *** )

standard protein-protein BLAST
Database: nr
Layout: One Window
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).

Step 2: Repeat the BLAST search with new parameters:

standard protein-protein BLAST
Database: nr
Limit by entrez query: Caenorhabditis elegans
Expect: 100
Descriptions: 1000
Layout: One Window
Other parameters: default

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

Step 3: Now repeat the search with PSI-BLAST ( BLAST at NCBI ):

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

After the first BLAST, run two PSI-BLAST iterations, with the same parameters, and then look at the result ( *** )and the taxonomy report ( *** ). How many insulin homologues did you find ?