BME355 Genomic Sequence Analysis End-of-Course Assessment – July Semester 2025, Singapore

INSTRUCTIONS TO STUDENTS:

1. This End-of-Course Assessment paper comprises SIX (6) pages (including the cover page).
2. You are to include the following particulars in your submission: Course Code, Title of the ECA, SUSS PI No., Your Name, and Submission Date.
   
3. Late submission will be subjected to the marks deduction scheme. Please refer to the Student Handbook for details.

IMPORTANT NOTE

ECA Submission Deadline: 10 November 2025, 12 noon

ECA Submission Guidelines

Please follow the submission instructions stated below:

This ECA carries 70% of the course marks and is a compulsory component. It is to be done individually and not collaboratively with other students. You must submit it on time.

Submission  

You are to submit the ECA assignment in exactly the same manner as your tutor-marked assignments (TMA), i.e. using Canvas. Submission in any other manner like hardcopy or any other means will not be accepted.

Electronic transmission is not immediate. It is possible that the network traffic may be particularly heavy on the cut-off date and connections to the system cannot be guaranteed. Hence, you are advised to submit your assignment the day before the cutoff date in order to make sure that the submission is accepted and in good time.

Once you have submitted your ECA assignment, the status is displayed on the computer screen. You will only receive a successful assignment submission message if you had applied for the e-mail notification option.

ECA Marks Deduction Scheme

Please note the following:

1. Submission Cut-off Time – Unless otherwise advised, the cut-off time for ECA submission will be at 12:00 noon on the day of the deadline. All submission timings will be based on the time recorded by Canvas.
2. Start Time for Deduction – Students are given a grace period of 12 hours. Hence calculation of late submissions of ECAs will begin at 00:00 hrs the following day (this applies even if it is a holiday or weekend) after the deadline.
3. How the Scheme Works – From 00:00 hrs the following day after the deadline, 10 marks will be deducted for each 24-hour block. Submissions that are subject to more than 50 marks deduction will be assigned zero mark. For examples on how the scheme works, please refer to Section 5.2 Para 1.7.3 of the Student Handbook.

Any extra files, missing appendices or corrections received after the cut-off date will also not be considered in the grading of your ECA assignment.

Plagiarism and Collusion

Plagiarism and collusion are forms of cheating and are not acceptable in any form of a student’s work, including this ECA assignment. You can avoid plagiarism by giving appropriate references when you use some other people’s ideas, words or pictures (including diagrams). Refer to the complete information on Harvard referencing and citation: http://www.open.ac.uk/libraryservices/documents/Harvard_citation_hlp.pdf You can avoid collusion by ensuring that your submission is based on your own individual effort. The electronic submission of your ECA assignment will be screened through a plagiarism detecting software. For more information about plagiarism and cheating, you should refer to the Student Handbook. SUSS takes a tough stance against plagiarism and collusion. Serious cases will normally result in the student being referred to SUSS Student Disciplinary Group. For other cases, significant marking penalties or expulsion from the course will be imposed.

Responsible Use of Generative AI tools  

While Generative AI tools such as ChatGPT can generate responses for you, it cannot understand the specific context of your assignment. This could result in irrelevant answers or errors which will impact negatively on your grades. If you must use these tools, it is your responsibility to check and validate the generated content and rephrase in your own words.

Remember that ideas and information taken from other sources, including those derived from the use of Generative AI tools such as ChatGPT, must be appropriately attributed. Note that Turnitin can detect both AI generated content and plagiarism, and you will be subject to the penalties outlined above.

For more information on the responsible use of generative AI tools and how to correctly cite them as a source, refer to SUSS Teaching and Learning Centre’s Academic Integrity course.

https://rise.articulate.com/share/GlQuywqm9MmZkxbaGig0HjjFA73k7aBr#/

Question 1

You have been assigned the task of determining the functional importance of the human MAOA gene. Arrange your findings in a logical format as you investigate the gene and answer the following questions. Include detailed screenshots to illustrate your process.

Question 1a

What is the full name and ID of the gene? Include detailed screenshots to support your answer.

(5 marks)

Question 1b

Using appropriate bioinformatics tools, demonstrate the exact location of the human MAOA gene on the chromosome. Illustrate in which human tissue does the gene shows the highest expression. Include detailed screenshots to support your answer.

(5 marks)

Question 1c

Discuss the function of this gene. Include detailed screenshots supporting  your answer.

(5 marks)

Question 1d

List any FIVE (5) pathways this gene is involved in using Reactome pathway database as the source. Include the detailed screenshots to support your answer.

(5 marks)

Question 2

Demonstrate your understanding in molecular genetics by critically evaluating the following statements.

Question 2a

Protein alignments are often preferred to DNA alignments.

(5 marks)

Question 2b

When comparing closely related proteins, it is advisable to use high value blosum matrices (BLOSUM90) and low value PAM matrices (PAM30).

(5 marks)

Question 2c

Position-Specific Iterated BLAST (PSI-BLAST) is often more sensitive than a regular BLAST search in finding distantly related protein sequences.

(5 marks)

Question 2d

The E-value is derived from Karlin-Altschul statistics. The higher the E-values, the more statistically significant is the BLAST result.

(5 marks)

Question 2e

Benchmarking is an important method for comparing different software tools and evaluating their accuracy.

(5 marks)

Question 3

Examine the given sequence using bioinformatics tools and answer the following questions:

melyetspyf yqeprfydge nylpvhlqgf eppgyertel tlspeapgpl edkglgtpehcpgqclpwac kvckrksvsv drrraatlre krrlkkvnea fealkrstll npnqrlpkveilrsaiqyie rlqallssln qeerdlryrg gggpqpgvps ecsshsascs pewgsalefsanpgdhllta dptdahnlhs ltsivdsitv edvsvafpde tmpn

Question 3a

Solve the identity of the sequence and the organism it belongs to. Using screenshots, discuss the steps used to determine its identity.

(10 marks)

Question 3b

Determine the function of the sequence and the conserved domains present in it. Include detailed screenshots to support your answer.

(5 marks)

Question 3c

List TWO (2) WikiPathways in which the corresponding gene is involved.

(5 marks)

Question 4

Using the sequence mentioned in Question 3, obtain its homologs (one each) from other organisms such as Pan troglodytes, Canis lupus dingo, Dasypus novemcinctus, Mus musculus and Rattus ratttus.

Question 4a

Paste the sequences in FASTA format.

(5 marks)

Question 4b

Create a multiple sequence alignment using any appropriate multiple sequence alignment tool, and include both the alignment and the corresponding phylogenetic tree in your answer.

(10 marks)

Question 4c

Evaluate the quality of the multiple sequence alignment and the accuracy of the phylogenetic tree derived from it. Provide justification for your evaluation.

(5 marks)

Question 5

Using   the       OMIM             database          information     for       Gastric             Cancer (https://omim.org/entry/613659), solve the following tasks:

Question 5a

Pull out the genes associated with gastric cancer and use the list as input in the online tool DAVID (Database for Annotation, Visualization and Integrated Discovery). Include the detailed screenshots in your answer.

(5 marks)

Question 5b

Perform a functional annotation clustering of the gene list and include screenshots of the results from GOTERM_BP/CC/MF_DIRECT and KEGG_PATHWAY.

(5 marks)

Question 5c

Appraise the results obtained and discuss how relevant the findings are to the gene list.

(5 marks)

—– END OF ECA PAPER —–