Môn học: Ứng dụng tin học trong CNSH - BIOINFORMATICS

Hướng dẫn học tập – Phần bài tập (Assignments)

A.1.2 - Group assignments
PhD. Truong Kim Phuong - 2023
1. Objectives
To learn and use the appropriate tools to collect data of target sequences as DNA, or RNA or
protein, then analyze the level of similarity and conduct the molecular phylogenetic analysis of
those sequences.
2. General requirements of the assignment
− Assignment A.1.2 is a type of project based learning
− Establish groups of students in which the number of members of each group ranges from 5 to 10
students.
− The total number of groups in each class is from 7 to 8 groups.
− Each group of students performs and completes the main requirements of this assignment
which are presented in Table 1 below, and need to take the following steps:
1. Download the full-text articles that have been provided in the reference list.
2. Randomly select a report topic corresponding to one of the articles mentioned above by
making the selection form on the LMS forum or video conferences.
3. Student groups download articles, read, and learn important information to prepare for
presentations of the chosen topic.
- Each group of students performs and completes the main requirements of this assignment
which are presented in Part 3 below as “Main requirements and questions of assignment”
- Present the data and analysis results obtained in a presentation.
− Language of the presentation of A.1.2 assignment: Vietnamese or English.
− Types of files are formated as PDF and PPT.
− Presentation report (PPT) must be complete and correct with the structure and layout as regulated
in Part “The structure of a PowerPoint presentation” below.
− Do not plagiarism.
− Show the references in the presentation.
− Students must complete and present a presentation report in class.
− Time for each presentation/each student group: 15 minutes; Interviews (questions – answers) of
each presentation: 10 minutes (If any presentation is too long, it will be stopped on time as this
regulation above). Time for submitting report files and making presentations will be announced on
the LMS. It is expected to the last lesson in week 6 of the course schedule.
❖ The structure of a PowerPoint presentation
− Slide 1: Must clearly state the school name, class name, subject, and your report topic. The
topic of the report is determined by the student group, based on the title and main content of
the reference article.
− Slide 2: List of members in the student group, including full name and student number.
− Slide 3: Show title and the objective and main content of the reference article.
− Slide 4 …: From slide 3 to the next slides, present the answers and demonstrate the results
according to the requirements and questions in Table 1 in part 3 above.
− - Slide for Conclusion: Present your conclusions, and summarize the results obtained and
present comments and suggestions on the topic being reported.
− Final slides: Show references, acknowledgement.
Note: The presented content must be clear, concise, accurate, and without spelling errors.

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 3. Main requirements and questions of assignment
− Summary of main requirements of the assignment: Identify the right data, use bioinformatics
tools/softwares for the building a phylogenetic tree of target sequences, and answers of the
following questions in Table 1 below. The target sequences are presented in the scientific article
that the student group has selected.
Table 1. Requirements and questions of assignment A.1.2
Scores
No Requirements and questions Notes
(points
Overview - Methodology
Describe the objective, methodology and overview of the reference article
I
(or this study) in your pressentation.
I.1 Define the objective of this study? 0.5
Define the target moleculars as gene as DNA sequences or mRNA sequences or
protein in this study?
Through search NCBI databases, find and show data:
I.2 1.25
- Accession number, length, other informations
- Roles of target molecular in cells, or host strain, host cells
- Role and/or the correlation of that target molecular in this study.
Summary the process in this study: material, methods and results.
In particular, students focus on two issues:
- Data of softwares, bioinformatic tools that are used in each study?
I.2 1.25
- The author's goal when using bioinformatics tools and conducting
molecular phylogenetic analysis?
- What do the results of analysis using bioinformatics tools reflect?
Apply bioinformatics tools to solve the assignment's requirements that is
analysis the level of similarity and conduct the molecular phylogenetic
II
analysis based on the sequences collected from the article.
Then, show the results in in your pressentation.
Separate file for
each sequence
and a file have
Through search NCBI databases as Genbank or GenPept, use their accession multiple
II.1 numbers for access and download the target sequences (DNA, RNA or protein) 2.0 sequence of a
in Fasta format same target
molecular
(Name of file:
....txt)
Perform a multiple sequence alignment of those sequences by the available
software, for example: Clustal W, etc.
II.2 1.5
Output the alignment’s results with format: “.aln”, etc, with name of file
as: Lipase gene_align_G6
Use Mega software for constructing the phylogenetics tree
- Find out phylogenetic models
- Bootstraps?
- Methods for phylogenetic analysis?
II.3 2.5
- Proofreading for phylogenetic analysis?
- Presentation phylogenetic trees that are made by student group
Read, identify and explain/discussion about the topology of phylogenetics trees
in this assignments and compare with the results of those references.
Conclusion
- Present some discussion ideas of student group about these analysis that
are conducted by students and compare with the results of those
III 1
references.
- Summarize the results obtained and present comments and suggestions
on the topic being reported.

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 4. References
No (Name of file) References
A1.2.Subject 1.1 Raco, M., Jung, T., Horta Jung, M., Chi, N. M., Botella, L., & Suzuki, N. (2023). Sequence
and phylogenetic analysis of a novel alphaendornavirus, the first virus described from the
oomycete plant pathogen Phytophthora heveae. Archives of Virology, 168(6), 1-7.
A1.2.Subject 2.1 Zhou, T. S., Zhou, R., Yu, Y. B., Xiao, Y., Li, D. H., Xiao, B., ... & Yang, Y. J. (2016). Cloning
and characterization of a flavonoid 3′-hydroxylase gene from tea plant (Camellia sinensis).
International Journal of Molecular Sciences, 17(2), 261.
A1.2.Subject 3.1 Luyen, V. T. (2017). Identification of the entomopathogenic fungi sample DL0069 by
combination of morphological and molecular phylogenetic analyses. Vietnam Journal of
Science and Technology, 55(1A), 117-117.
A1.2.Subject 4.1 Hossain, T. J. (2022). Genome-sequence, annotation and phylogenetic insights of the lactic
acid bacterium Limosilactobacillus fermentum strain LAB1 obtained from the dairy beverage
borhani. Available at SSRN 3996663.
A1.2.Subject 5.1 Huang, M., Guo, J., Jia, Y., Liao, C., He, L., Li, J., ... & Yu, Z. (2023). A Bacillus subtilis
Strain ZJ20 with AFB1 Detoxification Ability: A Comprehensive Analysis. Biology, 12(9),
1195.
A1.2.Subject 6.1 Demirci, M., Özge, Ü. N. L. Ü., & KOCAZEYBEK, B. (2021). In silico Analysis of Virulence,
Resistance Genes and Phylogeny of Helicobacter pylori Strains from Different Continents.
Experimed, 11(3), 170-178.
A1.2.Subject 7.1 Parvez, R., Vijayachari, P., Saha, M. K., Biswas, L., Ramasamy, J., Vins, A., ... & Nagarajan,
M. (2023). Distribution of Human Papillomavirus Genotypes among the Women of South
Andaman Island, India. Diagnostics, 13(17), 2765.
A1.2.Subject 7.1 Grami, E., Badawy, S., Kiljunen, S., Saidi, N., & Skurnik, M. (2023). Characterization and
genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia.
Archives of Virology, 168(2), 44.
A1.2.Subject 9.1 Dikson, D., Victor, H., Jong, D., Sanjaya, A., Samantha, A., Jo, J., & Pinontoan, R. (2022).
Whole-genome analysis of Bacillus subtilis G8 isolated from natto. Biodiversitas Journal of
Biological Diversity, 23(3).
A1.2.Subject 10.1 Zhang, Q., Balourdas, D. I., Baron, B., Senitzki, A., Haran, T. E., Wiman, K. G., ... & Joerger,
A. C. (2022). Evolutionary history of the p53 family DNA-binding domain: insights from an
Alvinella pompejana homolog. Cell Death & Disease, 13(3), 214.
A1.2.Subject 11.1 Rybak, B., Krawczyk, B., Furmanek-Blaszk, B., Wysocka, M., Fordon, M., Ziolkowski, P., ...
& Sikorska, K. (2022). Antibiotic resistance, virulence, and phylogenetic analysis of
Escherichia coli strains isolated from free-living birds in human habitats. PLoS One, 17(1),
e0262236.
A1.2.Subject 12.1 Gumaa, M. A., Idris, A. B., Bilal, N. E., & Hassan, M. A. (2021). First insights into molecular
basis identification of 16 s ribosomal RNA gene of Staphylococcus aureus isolated from
Sudan. BMC research notes, 14(1), 240.
A1.2.Subject 13.1 Nguyen, Q. H., Nguyen, T. T. H., Ha, T. L. A., Nguyen, T. U., Le Duc, V., Dang, T. L. A., ...
& Nguyen, V. S. (2023). Sequencing Analysis of COI Genes Isolated from Vietnam’s
Endemic Insect Species (Insecta: Plecoptera) for DNA Barcoding Database. VNU Journal of
Science: Natural Sciences and Technology, 39(3).
A1.2.Subject 14.1 Ravikumar, H., Ramachandraswamy, N., Sampathkumar, S., Prakash, B. M., Huchesh, H. C.,
Uday, J., & Puttaraju, H. P. (2010). A preliminary survey for Wolbachia and bacteriophage
WO infections in Indian mosquitoes (Diptera: Culicidae). Trop Biomed, 27(3), 384-393.
Note: The maximum number of articles studied in Assignment A.1.2 is 7-8 articles.

Good luck!
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