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Syllabus ( MBG 522 )


   Basic information
Course title: Bioinformatics
Course code: MBG 522
Lecturer: Assist. Prof. Saliha İŞSEVER ÖZTÜRK
ECTS credits: 7.5
GTU credits: 3 (3+0+0)
Year, Semester: 1/2, Fall and Spring
Level of course: Second Cycle (Master's)
Type of course: Area Elective
Language of instruction: Turkish
Mode of delivery: Face to face
Pre- and co-requisites: none
Professional practice: No
Purpose of the course: In this course, it is aimed that the students get to know the current bioinformatics methods and tools, learn the principles underlying these methods, use the methods and interpret the results.
   Learning outcomes Up

Upon successful completion of this course, students will be able to:

  1. Recognise biological databases.

    Contribution to Program Outcomes

    1. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Written exam
  2. Differentiate primary and secondary databases.

    Contribution to Program Outcomes

    1. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Written exam
    2. Homework assignment
  3. Search databases and retrieve information from them.

    Contribution to Program Outcomes

    1. Acquire scientific knowledge and work independently,
    2. Work effectively in multi-disciplinary research teams
    3. Understand the applications and basic principles of new instrumentation and/or software vital to his/her thesis projects.

    Method of assessment

    1. Homework assignment
    2. Laboratory exercise/exam
  4. Know pairwise and multiple sequence alignment algoritms and score matrices.

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Acquire scientific knowledge and work independently,
    3. Understand the applications and basic principles of new instrumentation and/or software vital to his/her thesis projects.

    Method of assessment

    1. Written exam
    2. Homework assignment
  5. Do similarity searches and interpret the results.

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Written exam
    2. Homework assignment
    3. Term paper
  6. Build up basic knowledge about protein structure.

    Contribution to Program Outcomes

    1. Identify structure-function relationships in cells and organisms
    2. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Written exam
    2. Homework assignment
    3. Term paper
  7. Predict secondary structures of proteins.

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Identify structure-function relationships in cells and organisms

    Method of assessment

    1. Laboratory exercise/exam
    2. Term paper
  8. Visualise 3D structures of proteins

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Identify structure-function relationships in cells and organisms
    3. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Laboratory exercise/exam
  9. Use protein identification and analysis tools.

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Laboratory exercise/exam
    2. Term paper
  10. Determine physico-chemical properties and also post-translational modifications of proteins.

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Homework assignment
    2. Laboratory exercise/exam
  11. Predict the function and structure of proteins.

    Contribution to Program Outcomes

    1. Define and manipulate advanced concepts of Biology
    2. Identify structure-function relationships in cells and organisms
    3. Acquire scientific knowledge and work independently,

    Method of assessment

    1. Homework assignment
    2. Laboratory exercise/exam
    3. Term paper
   Contents Up
Week 1: Introduction to the course

Introduction: Biological databases, bioinformatic resources and accessing the biological information
Week 2: Sequence comparison methods: Pairwise sequence alignment, database similarity searching, conservation of amino acids and score matrices
Week 3: Multiple sequence alignment methods and phylogenetic trees
Week 4: Protein families, motifs, patterns; secondary database searching; pattern, motif searching
Week 5: Protein sequence databases: Detailed study of SwissProt/TrEMBL, other sequence databases

Protein domain/family databases: Detailed study of ProDom and DOMO
Week 6: Protein domain/family databases: Detailed study of PROSITE and INTERPRO

Protein structure databases: PDB, MMDB, Swiss-3DIMAGE, etc.; specialized protein databases

Assignment 1
Week 7: Classification of proteins and prediction of secondary structures
Week 8: Midterm

Evaluation of the exam and solving the exam questions
Week 9: Classification of proteins according to secondary structures: CATH, SCOP
Week 10: Visualisation of the 3D structures of proteins

Week 11: Protein tertiary structure prediction
Week 12: Protein identification and analysis tools: EXPASY server

Assignment 2
Week 13: Gene and promoter prediction
Week 14: Student project presentation
Week 15*: General Evaluation
Week 16*: Final exam
Textbooks and materials:
Recommended readings: 1. Essential Bioinformatics. Xiong, J. Cambridge University Press, 2006.
2. Introduction to Bioinformatics. Lesk, A.M. (ed.). Oxford University Press, 2002.
3. Introduction to Bioinformatics: a Theoretical and Practical Approach. Krawetz, S.A. and Womble, D.D. (ed.). Humana Press, Totowa, New Jersey, 2003.
4. Bioinformatics: Genes, Proteins and Computers, Orengo, C.A., Jones, D.T. and Thornton, J.M. Garland Science/BIOS Scientific Publishers, New York, 2003.
5. Bioinformatics: Sequence and Genome Analysis. Mount, D.W. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, USA, 2004.
6. Structural Bioinformatics. Bourne, P.E. and Weissig, H. John Wiley, 2003.
7. Introduction to Protein Architecture: The Structural Biology of Proteins. Lesk, A. M. Oxford University Press, 2001.
8. Introduction to Protein Structure. Branden, C. and Tooze, J. Garland Pub., New York, 1999.
  * Between 15th and 16th weeks is there a free week for students to prepare for final exam.
Assessment Up
Method of assessment Week number Weight (%)
Mid-terms: 8 30
Other in-term studies: 0 0
Project: 14 10
Homework: 6, 12 10
Quiz: 0
Final exam: 16 50
  Total weight:
(%)
   Workload Up
Activity Duration (Hours per week) Total number of weeks Total hours in term
Courses (Face-to-face teaching): 3 8
Own studies outside class: 3 14
Practice, Recitation: 3 6
Homework: 6 2
Term project: 6 4
Term project presentation: 1 1
Quiz: 0 0
Own study for mid-term exam: 10 2
Mid-term: 10 2
Personal studies for final exam: 10 2
Final exam: 2 1
    Total workload:
    Total ECTS credits:
*
  * ECTS credit is calculated by dividing total workload by 25.
(1 ECTS = 25 work hours)
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