Assessment Task -1

The aim of this exercise is to help you deepen your understanding of homology analysis, and comprehend how to use various BLAST tools (e.g. TBLASTN, BLASTX, BLASTP) and various databases to discover novel genes.

• Select any protein of from an organism of your choice (critically justify the choice) and discover a “novel” gene in another organism that is homologous but has never been annotated before as related to your query. Therefore, you are discovering a new gene.
• Take your new gene/protein, name it, then search (using BLAST tools) it against databases to confirm it has not been described before.
• Prepare a written document structured with IMRAD format:
• State an aim and objectives for the specific analysis.
• Describe the methods you used coherently to enable replication
• Provide a critical justification for the method you used to perform the analysis.
• Coherently and logically present and interpret the results. Use figures and table where appropriate
• Critically discuss the findings. Cite in-text sources to justify your arguments
• Provide a complete reference list for the sources cited in your work

Assessment Task-2

Your primary aim is to determine the likely function of this new protein or how differences in the 3D structures might affect the functions of this new protein:

• Take your new gene/protein you discovered in Assessment A1.
• There are quite a few proteins that may be related this new protein and so you want to know the phylogeny of this new protein, identify possible orthologs and or paralogs, and compare their 3D structure(s) with that of the new protein..
• Perform multiple sequence alignment, phylogeny, and predict the protein’s structure and its function.

Cheat Guidance:

1. Generate a multiple sequence alignment with your novel protein, your original query protein, and a group of other members of this family. A typical number of proteins to use in a multiple sequence alignment is a minimum of 5 or 10 and a maximum 30, although the exact number is up to you.
2. Create a phylogenetic tree, using either a parsimony or distance based approach. Bootstrapping and tree rooting are optional. Use any program such as MEGAX, PAUP, or Phylip.
3. Compare the predicted structure of your protein to that of a known structure.
4. Show whether this gene is under positive or negative evolutionary selection.
5. Discuss the significance of your novel gene. What have you learned about this gene/protein family?

Assessment Task-3

In assignment A2, you examined the phylogeny and 3D structure of your novel protein. It is unclear whether possible variations in the DNA sequence of this protein has any biological consequences. Your aim is therefore to identify sequence variations contained in the DNA sequence of your novel protein identified in A1 through BLAST alignment, match it to highly informative records in dbSNP, and connect variations to functional analyses reported in literature to facilitate decision-making processes and enhance the speed and productivity of your research.

 Cheat guide:

1. Find single nucleotide polymorphisms in your novel gene
2. Use BLAST alignment to find the SNPs
3. Where are the location of the SNPs, what are the names of the SNPs, e.g.,?
4. Search dbSNP – what do we know about the SNPs you identified in your novel gene?
5. Discuss the impact of the SNPs on the predicted protein structure and function connect variations to functional analyses – how deleterious are the SNPs? what did you do (show evidence) to know the SNPs are or no not deleterious? how do the SNPs if at all affect the secondary and 3D structure of the predicted protein? how do you know the SNPs do not affect the secondary and 3D Structure of the predicted protein?
6. Write up your work using IMRAD format.

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