INSA - TP bioinformatique

Exercise 1: Retrieve informations in sequence databases

Step 1:

Objective: retrieve information on human insulin.

Search the human insulin gene in EMBL with WWW-Query at PBIL ( *** ). Use the following criteria:

Select Nucleotide databank, EMBL
Keyword: insulin
AND Species: homo sapiens
AND Type: CDS (to select the protein-coding region)
AND NOT Keyword: partial (to exclude incomplete sequences)

Retrieve the corresponding protein sequence in FASTA format ( *** ):

Sequence: protein
Format FASTA
Mode: direct sending

Go back two pages, and click on the link J00265.INS (note that this CDS results of the splicing of the insulin gene) ( *** ), and then J00265 (the complete insulin gene) ( *** ).

Click on the link 'PUBMED; 503234' to get bibliographic references in PubMed ( *** ).

Click on the link /protein_id="AAA59172.1" to retrieve the corresponding entry in SwissProt ( *** ). Note the location of insulin B an A chains and peptide C.

Click on the link 'InterPro; IPR004825' to retrieve the corresponding entry in INTERPRO ( *** ).

Click on the link 'PROSITE; PS00262' to retrieve information on the insulin protein signature in PROSITE ( *** ).

Step 2:

Objective: retrieve all mammalian insulin proteins.

Use WWW-Query at PBIL to search for all mammalian insulin protein in Uniprot/SwissProt. Extract sequences in FASTA format.

NB: you can use the wildcard "*" to specify any series of characters to catch several keywords in one shot. For example: "*insulin" will catch "insulin, proinsulin, preproinsulin, etc.".

NB: take care not to include "insulin receptors", "insulin like growth factor", etc. in your selection.