MOLECULAR BIOLOGY AND DIAGNOSTICS LABORATORY

INFORMATION RETRIEVAL FROM ONLINE BIOLOGICAL DATABASES

Learning outcomes

At the end of this exercise the student should be able to

1) Visit the commonly used bioinformatics websites
2) Correctly identify the database that will give the data for the gene that he or she is
studying
3) Retrieve molecular data from NCBI Gene, Nucleotide, Genome, PubMed
4) Organize and process the retrieved information into a comprehensive output.

Materials and Methods

The instructor will introduce the students to the commonly used bioinformatics websites:
(already done during the first meeting)

 NCBI http://www.ncbi.nlm.nih.gov/

 Psi-Phi BLAST http://www.ncbi.nlm.nih.gov/BLAST/

 Clustal Omega http://www.ebi.ac.uk/Tools/msa/clustalo/

 ExPASy http://us.expasy.org/

 SwissProt http://us.expasy.org/sprot/

List of gene choices

Gene Name Full Name
1 TP53 Tumour-suppressor p53
2 TNF Tumour necrosis factor
3 EGFR Epidermal growth factor receptor
4 VEGFA Vascular endothelial growth factor A
5 APOE Apolipoprotein E
6 IL6 Interleukin 6
7 TGFB1 Transformation growth factor beta 1
8 MTHFR Methylenetetrahydrofolate reductase
9 ESR1 Oestrogen receptor 1
10 CD4 T-cell receptor protein

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Instructions

1) Name of Gene that was assigned (Full name and symbol)

2) What is the source of the gene that you have chosen (prokaryotic or eukaryotic? Name
of organism

3) Is the gene protein-coding, non-coding, regulatory, and others

4) Describe the function of the gene or the gene product (the gene product is the protein)
Describe clearly the function. Do not lift the words directly from the database; write in
your own words

5) Search for the nucleotide sequence of the gene in the Nucleotide database of NCBI.
Look for the mRNA linear or complete cdsThis can be identified by the “mRNA linear”
or “complete cds” keywords in the GenBank entry for the gene. Include the complete
coding nucleotide sequence of the gene in the profile.

6) Look for the gene structure where in the number of bases, no of exons/ introns,
untranslated regions (UTR), etc are described.

7) Describe the structure of the gene product (use UniProtKB for this criteria).

8) Search the complete amino acid sequence of the gene by using either the GenBank or
the UniProtKB data sheet and include it in your Gene profile. How many amino acids are
in the gene/ protein product.

9) Copy the amino acid code from answer from above and go to prosite.expasy.org and
search for motifs in the amino acid sequence.

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Name:____________________________ Section:____________ Date: _____________
Name of Gene:
Is it exclusively a Prokaryotic or
Eukaryotic gene?

Gene type

Function of the gene product

Location in the genome:

Gene structure:

Nucleotide sequence (genomic

and mRNA):

Structure of gene product:

Amino acid sequence:

Motifs in the polypeptide

sequence: