Protein Sequence By Bioinformatics Methods Assessment Answer

Assignment Task:

Introduction:
You are required to analyse a protein sequence by bioinformatics methods. What is its likely function? If it does not have a structure can you determine a model for the structure? What does the model tell you about its function? It might also be a "hypothetical" protein, where the structure has already been determined by a structural genomics consortium. In which case can you use sequence and known structure to determine protein function? You are not restricted to methods covered in the lectures, but you should focus on methods with the general aim of prediction of protein function and/or structure from sequence. You can either request a sequence to the module manager or chose your own.

Questions you might want to think about before choosing a protein:

1. Use this assessment to do an in-depth analysis of a protein (or protein family) that interests you and/or for which there is an interesting biological question.

2. Use it to pull out new protein family members (e.g. to those of a well-characterized family of proteins) that are not found by BLAST/FASTA.

3. Use it to try out some new tools that we were unable to cover in the course. 

4. Use it to increase your depth of knowledge of tools that we have covered in the course e.g. structure prediction methods (comparative modelling or fold recognition) and try to relate the structure you get to its known function - e.g. active site, binding site etc. 

5. Use it to study a protein that has recently appeared in the scientific press (Nature, Science, New Scientist) or even the daily press! If it is not already highly characterized (and in some cases, it may well be) then there may be an interesting bioinformatics story to be told or new and different analyses that can be done. 

6. If you are interested in the protein family then there are family tools we have looked at (ClustalW, JalView Pfam). 

7. If you are interested in finding new proteins related to your protein of interest in other organisms then PSI-BLAST and Hidden Markov techniques such as HMMER or SAM may be useful

8. If you have a transmembrane spanning protein- there are programs you can use to predict TM helices etc. (e.g. TMpred, Memsat, DAS etc.)

Do you need to get structural information in order to answer the biological questions you are asking? If so you should check either you can make a comparative model OR get meaningful information from fold recognition before you proceed with your chosen protein.

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