Bioinformatics and Functional Genomics (BFG) Assessment 3 - Brief & Criteria

BFG Assessment 3 - Brief and Criteria

Assessment 3: Assigning Functions to Polymorphisms

Assessment Details

Assessment Type: Written Assignment
Weighting: 40% of module grade
Submission Deadline: Week 12
Submission Method: Turnitin via Blackboard Word Count: 1500 words
Feedback Date: 3 weeks from submission

Assessment Overview

In this assessment, you are asked to write an assignment performing bioinformatics analyses to identify and characterize genetic variations in specific genes or genomic regions. You will use in silico analysis methods to identify variations, map them to dbSNP, connect them to functional analyses, and critically discuss their clinical implications for phenotypes and/or diseases.

This assessment integrates your learning from across the module and requires you to apply multiple bioinformatics approaches to a clinically relevant problem.

Learning Outcomes Assessed

This assessment addresses the following module learning outcomes:

LO1: Apply in-depth knowledge on a range of bioinformatics C 'omics analysis tools, resources C databases to analyse DNA, RNA and Protein Sequences
LO2: Demonstrate proficiency in the application of computational methods to design the collection and interpret experimental and clinical data
LO3: Communicate complex knowledge and understanding of biotechnology in the context of its underlying theoretical basis with an emphasis on the technologies routinely used in genomics, proteomics and metabolomics
LO4: Use and/or implement a suite of core bioinformatics tools/services and evaluate their application

Assessment Task

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.

Guide:

1.Find single nucleotide polymorphisms in your novel gene, use BLAST alignment tool.

Option A: If multiple sequences exist in databases - Retrieve all available sequences of your gene from different individuals/populations - Perform multiple sequence alignment - Identify variable positions (SNPs)
Option B: If only one sequence exists - Use BLAST to find closely related sequences - Identify differences as potential variants - Acknowledge these are interspecies differences, not true SNPs
Option C: Use existing variant databases - Check if your gene/organism has variant data in dbSNP, gnomAD, or similar - If no data exists, focus on predicted variants from sequence comparison

2.Where are the locations of the SNPs, what are the names of the SNPs?

3.Search dbSNP – what do we know about the SNPs you identified in your novel gene?

4.Discuss the impact of the SNPs on the predicted protein structure and function connect variations to functional analyses:

1. How deleterious are the SNPs?
2. What did you do (show evidence) to know the SNPs are or no not deleterious?
3. How do the SNPs if at all affect the secondary and 3D structure of the predicted protein?
4. How do you know the SNPs do not affect the secondary and 3D Structure of the predicted protein? Etc.

5.Write up your work using IMRAD format.

Important Considerations:

-If your novel gene is truly novel, it may NOT be in dbSNP yet. You may need to simulate variants or use closely related species' data.
-For non-model organisms, variant data is often limited
-Acknowledge these limitations in your discussion

Assessment Criteria s Rubric

Academic Integrity

All work submitted must be your own. This includes:
-Your own bioinformatics analysis (not copied from papers or classmates)
-Proper citation of tools, databases, and literature used
-No use of essay mills or unauthorized AI assistance

Suspected academic misconduct will be investigated under university regulations and may result in penalties including failure of the assessment or module.

Submission Instructions

1. Save your document as: StudentID_BFG_A3_Surname_Firstname.docx or .pdf
2. Upload to Blackboard via the Assessment 3 Turnitin submission link by the deadline
3. Ensure file uploads successfully - you'll receive a confirmation email

Feedback Within 3 weeks of submission

You will receive:

-Rubric scores for each criterion
-Written comments highlighting strengths and areas for improvement