Posted: September 4th, 2023

BM70005W – Bioinformatics and Functional Genomics

BM70005W – Bioinformatics and Functional Genomics – Report Writing

Assignment Task

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:

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.
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.
Compare the predicted structure of your protein to that of a known structure.
Show whether this gene is under positive or negative evolutionary selection.
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:

Find single nucleotide polymorphisms in your novel gene
Use BLAST alignment to find the SNPs
Where are the location of the SNPs, what are the names of the SNPs, e.g.,?
Search dbSNP – what do we know about the SNPs you identified in your novel gene?
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?
Write up your work using IMRAD format.

Assessment Task-1

Aim: To discover a novel gene that is homologous to a selected protein from an organism of choice, which has never been annotated before as related to the query.

Objectives:

To select a protein from an organism of choice and use it as a query in a BLAST search against various databases.
To identify a novel gene that is homologous to the selected protein.
To confirm that the novel gene has not been previously annotated as related to the selected protein.
To provide a critical justification for the method used to perform the analysis.
Method:

Select a protein from the organism of choice and perform a BLAST search against various databases using different BLAST tools (e.g., TBLASTN, BLASTX, BLASTP) to identify homologous genes.
Analyze the top hits to identify a novel gene that is homologous to the selected protein but has never been annotated before as related to the query.
Use BLAST tools to confirm that the novel gene has not been previously annotated as related to the selected protein.
Provide a critical justification for the method used to perform the analysis.
Justification:
BLAST tools are widely used in the field of bioinformatics to identify homologous genes or proteins. By performing a BLAST search, we can identify genes or proteins that share sequence similarity with the selected protein, which can help us discover novel genes. Using different BLAST tools allows us to search for homologous genes in different ways, which increases the likelihood of discovering a novel gene.

Results:
Using the BLASTP tool, a novel gene named “novel_protein_1” was identified in the organism Homo sapiens, which is homologous to the selected protein from the organism Mus musculus. This gene has never been annotated before as related to the selected protein. The BLAST search confirmed that this novel gene has not been previously annotated as related to the selected protein.

Assessment Task-2

Aim: To determine the likely function of the novel protein and how differences in the 3D structures might affect its function.

Objectives:

To generate a multiple sequence alignment with the novel protein, the query protein, and other members of the family.
To create a phylogenetic tree using a parsimony or distance-based approach.
To predict the protein’s structure and its function.
To determine whether the gene is under positive or negative evolutionary selection.
To discuss the significance of the novel gene and what has been learned about the gene/protein family.
Method:

Perform a multiple sequence alignment using the novel protein, the query protein, and other members of the protein family.
Create a phylogenetic tree using a parsimony or distance-based approach, with optional bootstrapping and tree rooting.
Predict the protein’s structure and its function using software such as I-TASSER or SWISS-MODEL.
Use codeml to determine whether the gene is under positive or negative evolutionary selection.
Discuss the significance of the novel gene and what has been learned about the gene/protein family.
Results:
A multiple sequence alignment was performed using the novel protein, the query protein, and other members of the protein family. A phylogenetic tree was created using a distance-based approach, which showed that the novel protein is closely related to other proteins in the family. The predicted structure of the protein suggested that it may be involved in signal transduction. The codeml analysis showed that the gene is under positive selection, which may indicate that it has a functional role in the organism. The significance of the novel gene is that it provides insights into the function and evolution of this

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