Bioinformatics and Functional Genomics (BFG) Assessment 2: Phylogenetic and Protein Prediction Analysis

BFG Assessment 2 - Brief and Criteria

Assessment 2: Phylogenetic and Protein Prediction Analysis

Assessment Details

Assessment Type: Written Assignment
Weighting: 40% of module grade
Submission Deadline: Week 10
Submission Method: Turnitin via Blackboard
Word Count: 1500 words
Feedback Date: 3 weeks from submission

Assessment Overview

In this assignment, you are asked to determine the likely function of your novel protein discovered in Assessment 1 and analyse how differences in 3D structures might affect the functions of this protein. You will use multiple sequence alignment, phylogenetic analysis, protein structure modelling, and functional prediction tools to comprehensively characterize your protein of interest.
This assessment builds directly on Assessment 1 and allows you to demonstrate deeper analysis using advanced bioinformatics tools.

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

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 to 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.

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 known structures:

1. Use SWISS-MODEL, Phyre2, or AlphaFold to predict your novel protein's structure 4.
2. Find experimentally determined structures of homologs in PDB
3. Identify conserved structural features (active sites, domains, motifs)
4. Discuss structural differences and their functional implications

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?

What you should demonstrate:

-Your novel gene clusters with the expected protein family
-Orthologs vs paralogs are correctly identified
-Structural predictions are reasonable and interpreted
-Evolutionary patterns make biological sense
-Any anomalies are discussed (e.g., long branch, unexpected clustering)

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_A2_Surname_Firstname.docx or .pdf
2. Upload to Blackboard via the Assessment 2 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