Prepare project report on "An investigation of the protein sequence and protein domains".

Session 1 - Learning about the protein sequence and investigation of protein domains.

1. Use your protein sequence reference code and get information about your protein

2. Look through the files locating the number of amino acids present and the function of your protein. Also look for any other important information.

3. Write in your lab book a reasonable amount about what you have found within the (Uniprot file)

4. Cross-links to the different Family and domain databases and ascertain the domains present within your protein and the amino acids present within those domains. (Graphical view in Smart and Pfam databases works well). Make a note of these. Do the different domain databases give similar results in terms of domains found and the amino add residues present within those domains?

5. Take a look at the protein-protein interactions of your protein and what drug it interacts with, if any.

Use a notebook to record all of your findings. This is your logbook and needs to be submitted later as an item of assessment. Therefore make sure you write up result comprehensively. Each entry made in logbook should be a dated entry.

Session 2

1. Run protein-protein BLAST for your sequence. Websites for BLAST either at NCBI or EBI.

2. Run against both a protein sequence database i.e. SWISS-PROT part of Uniprot and the protein DataBank (pdb) - 2 independent runs.

3. Either printout or save html output files.

4. Read through HELP facilities at BLAST sites and attempt to understand how to interpret the output produced.

5. Be ready to discuss output from BLAST.