| Academic Unit: |
Molecular Biology and Genetics |
| Mode of Delivery: |
Face to face |
| Prerequisites: |
None |
| Language of Instruction: |
English |
| Level of Course Unit: |
Undergraduate |
| Course Coordinator: |
- - |
| Course Objectives: |
This course aims to deliver an introduction to computational methodologies for analyzing DNA, RNA and protein data, databases and access to information. It briefly introduces the basic principles behind sequence analysis and protein structure determination. |
| Course Contents: |
The lecture starts with the collection and storage of all types of biological sequences. The techniques behind the pairwise alignments of sequences are then introduced and followed by the probability and statistical analysis of sequence alignment. The two most popular sequence database search techniques, BLAST and FASTA, are introduced. In the second section, fundamentals of protein structure were introduced alongside experimental tools such as NMR and x-ray crystallography. Information retrieval from databases. Graphics visualization tools such as PyMOL and VMD are presented. Algorithms for predicting the secondary and tertiary structure of proteins such as homology modeling and fold-recognition are introduced. |
| Learning Outcomes of the Course Unit (LO): |
- 1- Ability to access and store sequences
- 2- Ability to perform pairwise sequence alignment, basic knowledge about the statistical analysis of sequence alignment results
- 3- Ability to search databases for similar sequences using BLAST and FASTA tool
- 4- Basic knowledge of protein structure
- 5- Able to use at least one molecular visualisation tool
- 6- Basic knowledge of the algorithms for predicting secondary and tertiary structure
- 7- Able to infer protein function from structure
- 8- Basic knowledge of homology modelling, fold recognition and ab initio techniques
|
| Planned Learning Activities and Teaching Methods: |
Two midterm exams, one final exam, and Homeworks (Exercises) |
| Week | Subjects | Related Preperation |
| 1 |
Basic knowledge about the history of scientific developments that led to current bioinformatics |
Reading the related chapter from textbook |
| 2 |
Access to databases, data types |
Reading the related chapter from textbook |
| 3 |
Pairwise sequence alignment: Scoring Matrices (PAM, BLOSUM) |
Reading the related chapter from textbook |
| 4 |
Pairwise sequence alignment: statistical analysis |
Reading the related chapter from textbook |
| 5 |
Advanced database searching for similar sequences, FASTA,BLAST |
Reading the related chapter from textbook |
| 6 |
Midterm I |
Study of the related chapters covered in the first five weeks |
| 7 |
Fundamentals of protein structure |
Reading the related chapter from textbook |
| 8 |
Molecular Visualization Tools: PyMOL, VMD |
Reading the related chapter from textbook |
| 9 |
Secondary Structure Assignment |
Reading the related chapter from textbook |
| 10 |
Inferring Protein Function from Structure |
Reading the related chapter from textbook |
| 11 |
Homology Modelling |
Reading the related chapter from textbook |
| 12 |
Threading and Ab Initio Methods |
Reading the related chapter from textbook |
| 13 |
Midterm II |
Study of the related chapters covered in the last six weeks |
| 14 |
Final Review |
Study of the chapters covered in the whole semester |
At Kadir Has University, a Semester is 14 weeks; The weeks 15 and 16 are reserved for final exams.
THE RELATIONSHIP BETWEEN COURSE LEARNING OUTCOMES (LO) AND PROGRAM QUALIFICATIONS (PQ)
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PQ1 |
PQ2 |
PQ3 |
PQ4 |
PQ5 |
PQ6 |
PQ7 |
PQ8 |
PQ9 |
PQ10 |
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| LO5 |
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| LO6 |
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| LO7 |
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| LO8 |
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Contribution: 1 Low, 2 Average, 3 High
