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| MBG2020 | Bioinformatics | 2+2+0 | ECTS:5 | | Year / Semester | Spring Semester | | Level of Course | First Cycle | | Status | Compulsory | | Department | DEPARTMENT of MOLECULAR BIOLOGY and GENETICS | | Prerequisites and co-requisites | None | | Mode of Delivery | | | Contact Hours | 14 weeks - 2 hours of lectures and 2 hours of practicals per week | | Lecturer | Prof. Dr. Yusuf BEKTAŞ | | Co-Lecturer | No | | Language of instruction | Turkish | | Professional practise ( internship ) | None | | | | The aim of the course: | | It is aimed that these students learn the bioinformatics discipline. It is the aim of this course to introduce current bioinformatics methods and tools that can be used for analyzing the data obtained, to introduce the database of biological data and other biological information sources, to access the data in these sources, and to teach the basic principles underlying these methods. |
| Learning Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | LO - 1 : | To have knowledge about definition, scope and history of bioinformatics field | 5 | 1, | | LO - 2 : | They can have information about various biological databases and can access the biological data by scanning these databases. | 5 | 1,4, | | LO - 3 : | They can recognize binary and multiple sequence alignment algorithms and score matrices. | 5 | 1,4, | | LO - 4 : | They can do similarity scores and interpret the results | 5 | 1,3,4, | | LO - 5 : | They can design their own primers in line with their requirements | 5 | 1,4, | | LO - 6 : | They can make restriction analyzes | 5 | 1,4, | | LO - 7 : | They can identify and search primary and secondary protein databases (protein sequence, domain / family and structure databases) | 5 | 1,4, | | LO - 8 : | They can determine the physico-chemical properties and post-translational modifications of proteins | 5 | 1,4, | | CTPO : Contribution to programme outcomes, TOA :Type of assessment (1: written exam, 2: Oral exam, 3: Homework assignment, 4: Laboratory exercise/exam, 5: Seminar / presentation, 6: Term paper), LO : Learning Outcome | | |
| Access to databases frequently used in molecular biology, genetics and nearby areas, homology comparison of genes and proteins, primer design, molecular applications, restriction-map generation, structure estimation, phylogenetic tree creation. |
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| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Definition, Scope and History of Bioinformatics | | | Week 2 | Biological Databases and Access to Information I, Biological Databases and Information Access II, Collection and Storage of Sequences: Submission of Sequences to Databases; Sequences Formats | | | Week 3 | Analyzes with a single DNA sequence | | | Week 4 | Protein amino acid sequence databases | | | Week 5 | Analyzes with a single protein amino acid sequence | | | Week 6 | Similarity studies in sequence databases | | | Week 7 | Comparison of two sequences | | | Week 8 | Multiple sequence alignment | | | Week 9 | Mid-term exam | | | Week 10 | Protein Analysis | | | Week 11 | Imaging of 3-dimensional structures of proteins: RasMol, Swiss-PdbViewer | | | Week 12 | Primer Design (PCR Principles, FASTPCR) | | | Week 13 | Restriction Analyzes (Restriction Enzymes: General Information, REBASE) | | | Week 14 | Phylogenetic tree creation | | | Week 15 | General assessment | | | Week 16 | Final Exam | | | |
| 1 | Biyoenformatik I Dizi Kıyaslamaları. JENS ALLMER Nobel Yayıncılık 2012 ISBN:978-605-133-297-0 | | | |
| 1 | Bioinformatics and Molecular Evolution. Higgs, Paul G. and Attwood, Teresa K. Blackwell Pub., Malden, MA, 2005. | | | 2 | Bioinformatics: Sequence and Genome Analysis. Mount, D. W. Cold Spring Harbor Laboratory Press, New York, 2001. | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 9 | 1 | 2 | 30 | | Homework/Assignment/Term-paper | 7
15 | 1 | | 20 | | End-of-term exam | 16 | 1 | 3 | 50 | | |
| Student Work Load and its Distribution | | Type of work | Duration (hours pw) | No of weeks / Number of activity | Hours in total per term | | Yüz yüze eğitim | 2 | 14 | 28 | | Sınıf dışı çalışma | 20 | 1 | 20 | | Arasınav için hazırlık | 30 | 1 | 30 | | Arasınav | 2 | 1 | 2 | | Ödev | 40 | 2 | 80 | | Dönem sonu sınavı için hazırlık | 30 | 1 | 30 | | Dönem sonu sınavı | 2 | 1 | 2 | | Total work load | | | 192 |
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