Bioinformatics Database and Software Resources CAL Assignment 1

Bioinformatics (Molecular Medicine) [2025] CAL Assignment 1 (30%)

Learning outcomes:

At the end of this CAL assignment, students should be able to:

• search entry in various database
• acquire information from various database
• produce written report

Using suitable database and knowledgebase, students are expected to provide information from the perspective of genomic and proteomic, on the “SpoIVB peptidase”. Students should provide relevant evidence from the search (figures, downloadable data files and etc) too to support the results (Part 1 and Part 2). Students should compare the results from the different databases that were used and describe the difference between them. Students are encouraged to further reflect on the suitability of the databases in acquiring information.

Subsequently, students are expected to use suitable resources to explore the impact of somatic mutations in human cells. The questions were listed in CAL Tutorial 1 (Part 3). Answer all questions and attach relevant evidence from the search to support the results.

Dateline for submission is 28 Sep 2025, 11.59pm MYT via E-learn/ ODL portal.

Marking Rubric for CAL Assignment 1

Utilization of Structural Information for Medical Sciences (BBT 2355)

Prepared by YWK

In this CAL tutorial, students will learn how to effectively utilise and evaluate Bioinformatics database and resources to discover biological data in genomics, proteomics and other related omics.

Part 1:

Learning Outcome:

At the end of this CAL tutorial, students are expected to:

• search entry in various NCBI database
• acquire information in various NCBI database

1. Using “SpoIVB peptidase” as example, search in the NCBI Pubmed database
   (https://pubmed.ncbi.nlm.nih.gov/) to get this information:
   • How many abstracts are returned?
   • What does each record contain? (Hint: just click on the links).
   • Click on any of the articles.
     • Who are the authors?
     • What is the title?
     • What is the journal; which volume, issue (if any) and page numbers?
     • What is the PubMedID (PMID)?
     • How is this article related to SpoIVB peptidase? (Hint: Read the abstract by clicking on the hyperlinked journal title)
     • Download the citation text using AMA format. (upload)
   • On which year is the oldest article among the results returned published? (Hint:
     You may need to select the option to show 200 items per page and sort by publication date: Display Settings → Items per page set to “200” and Sort by “Pub Date”).
2. Using “SpoIVB peptidase” as example, search in the NCBI Protein database
   (https://www.ncbi.nlm.nih.gov/protein/) to get this information:
   • How many hits are there?
   • How many hits are from bacteria? Fungi? Protists?
   • How many entries found from Bacillus thuringiensis?

   a. Look for “SpoIVB peptidase [Caldibacillus thermoamylovorans]”

   • List the following: Accession number, version number, total number of residues found, which organism is this SpolVB peptidase from, which authors produced this entry, EC number of this entry and protein sequence of this entry

   b. Identify the conserved region of this entry:

   • How many conserved region is found?
   • What is the accession number?
   • Name the protein classification.
   • Name 1 description of the conserved region
3. Using “SpoIVB peptidase” as example, search in the NCBI Nucleotide database
   (https://www.ncbi.nlm.nih.gov/nucleotide/ ) to get these information:
   • How many hits are there?
   • How many hits are from bacteria? Fungi? Protists?
   • How many entries found from Bacillus thuringiensis?
4. Look for “Bacillus paralicheniformis strain BL-09, complete genome”
   • List the following: GenBank number, version number, total number of base pair, which organism is this entry from, which authors produced this entry, is this from DNA or RNA? What is the nucleotide sequence of this entry
5. How many genes are found?
6. Look for a protein name “DNA polymerase III subunit beta”
   • Which gene codes for this protein?
   • What is the protein ID?
   • List the protein sequence.

Part 2:

Learning Outcome:

At the end of this CAL tutorial, students are expected to:

• search entry in UniProtKB knowledgebase

1. Using “SpoIVB peptidase” as example, search in the NCBI database to get these information:
   • How many total entries found? How many in Swiss-Prot? How many in TrEMBL?
   • How many entries found from Bacillus subtilis?
2. Look for “O35002 (CTPB_BACSU)”
   • Name the protein name, gene name, organism, function of this entry, how many active sites, what biological processes that is involved? Taxonomic lineage, how many mutations?
3. Name 4 proteins that share similarity with this entry.
4. Download the FASTA file of this entry (upload)
5. Name each mutation incidents found in this entry.

https://www.ncbi.nlm.nih.gov/nucleotide/

Part 3:

Learning Outcome:

At the end of this CAL tutorial, students are expected to:

• search entry in COSMIC

COSMIC (https://cancer.sanger.ac.uk/cosmic ), the Catalogue of Somatic Mutations In Cancer, is the world’s largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer.

Use tutorial videos listed in https://cancer.sanger.ac.uk/cosmic/help/tutorials to help you to understand and use COSMIC in a more effective way.

Using the “Cancer Browser”, perform and answer the following questions:

1. Select “Eye” at the Tissue Selection and “Conjunctiva” at Sub-Tissue, list the total results and indicate which histology levels they are found in.
2. Select “Squamous cell carcinoma” at sub-histology selection and show detail information for this specific cancer. Which genes are found to be associated with this cancer?
3. List the different types of mutations and its associated percentages found in the experimental samples for the genes in Question 2.
4. List the observed substitution mutations where the nucleotide change is known for the genes in Question 2.
5. Show how we could find out more about the genes listed in Question 2.
6. Show how we could see if there is(are) drug(s) associated with the gene resistance mutations. Please show in screenshots on how we could obtain this information.
7. Search “EGFR” using the Cancer Gene Census, list other cancers are associated with this gene.
8. Explain how EGFR gene is involved in cancer progression using the information found in Hallmarks of Cancer.
9. Does EGFR promote or suppress a process related to cancer? How do you know?
10. Explain how COSMIC database is useful in understanding somatic mutation in a particular cancer.

Answer

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