BME355 ECA (End-of-Course Assessment) : July Semester 2024 – Genomic Sequence Analysis

Question 1

You have been assigned the task of determining the functional importance of the human CDK1 gene. Investigate the gene and answer the following questions.

Question 1a

Determine the full name and ID of the gene.

Question 1b

Assess the chromosome it is found on and the tissue which shows the highest expression.

Question 1c

Discuss the function of this gene.

Question 1d

Using Reactome pathway database as the source, list any FIVE (5) pathways which this gene is involved in.

Question 2

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

>testseq

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Question 2a
Solve the identity of the sequence and the organism it belongs to. Create screenshots to record the steps used to determine its identity.

Question 2b
Determine the function of the sequence and the conserved domains present in it.

Question 2c
Identify the pathways which the corresponding gene is involved in.

Question 3

Using the sequence mentioned in Question 2, obtain its homologs (one each) from other organisms such as Pan troglodytes, Pan paniscus, Canis lupis familiaris, Mus musculus and Rattus norvegicus.

Question 3a
Assemble the sequences in FASTA format.

Question 3b
Create a multiple sequence alignment from your answer in Question 3a. Show the alignment results and the corresponding phylogenetic tree.

Question 3c
Evaluate the alignment and the phylogenetic tree.

Question 4

Using the OMIM database information for Lung Cancer (https://omim.org/entry/211980), solve the following tasks:

Question 4a

Identify the genes associated with Lung Cancer and use them as input data in the online tool DAVID (Database for Annotation, Visualization and Integrated Discovery). Show your working.

Question 4b

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

Question 4c

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

Question 5

Demonstrate your understanding in molecular genetics and critically appraise the following statements.

Question 5a
Protein alignments are often more informative than DNA alignments.

Question 5b
When comparing two sequences, it may be necessary to repeat the search using different scoring matrices.

Question 5c
Position specific iterated BLAST (PSI-Blast) is often less sensitive than a regular Blast search in finding distantly related protein sequences

Question 5d
The statistical significance of a BLAST result cannot be assessed through Evalues.

Question 5e
Benchmarking is an important approach to compare different software and determine their accuracy.

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