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| MBGL5030 | Advanced Bioinformatics | 3+0+0 | ECTS:7.5 | | Year / Semester | Spring Semester | | Level of Course | Second Cycle | | Status | Elective | | Department | DEPARTMENT of MOLECULAR BIOLOGY and GENETICS | | Prerequisites and co-requisites | None | | Mode of Delivery | | | Contact Hours | 14 weeks - 3 hours of lectures per week | | Lecturer | Doç. Dr. Halil İbrahim GÜLER | | Co-Lecturer | No | | Language of instruction | Turkish | | Professional practise ( internship ) | None | | | | The aim of the course: | | The aim of this course is to provide knowledge on the use of bioinformatics programs and in silico applications in processing biological information for students in biology, molecular biology, as well as those pursuing postgraduate education in other life sciences and engineering disciplines, but with a non-biological background. The course covers topics such as regional and global sequence alignment using score matrices (PAM, BLOSUM), multiple sequence alignment algorithms, database search algorithms (Blast, Fasta), distance matrices, phylogenetic tree construction, protein modeling, motif identification, molecular docking studies, and primer design studies. |
| Programme Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | PO - 1 : | To learn about DNA data and sequence matching | 2,6 | 1,4, | | PO - 2 : | To learn about prediction methods of DNA regulatory regions | 2,6 | 1,4, | | PO - 3 : | To learn the bioinformatic analysis of proteins | 2,6 | 1,4, | | PO - 4 : | To be able to use various bioinformatics programs | 2,6 | 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), PO : Learning Outcome | | |
| The content of the course includes regional and global sequence alignment using score matrices (PAM, BLOSUM), multiple sequence alignment algorithms, database search algorithms (Blast, Fasta), distance matrices, phylogenetic tree construction, protein modeling, motif identification, molecular docking studies, and primer design. It covers the instruction on the use of bioinformatics programs and online bioinformatics tools. |
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| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Sequence data formats and features | | | Week 2 | Searching DNA datas and databases | | | Week 3 | Database search with heuristic approaches | | | Week 4 | The basics of sequence alignments and algorithms | | | Week 5 | Prediction of promoter regions and transcription factors | | | Week 6 | Prediction of ORF regions | | | Week 7 | Determination of translation initiation sites | | | Week 8 | Mid-term exam | | | Week 9 | Data submission to Genbank | | | Week 10 | Phylogenetic trees | | | Week 11 | Softwares used for constructing phylogenetic trees | | | Week 12 | Protein databases | | | Week 13 | Domain and Motif estimation | | | Week 14 | Primer design | | | Week 15 | Molecular Docking | | | Week 16 | End-of-term exam | | | |
| 1 | Bioinformatics and Functional Genomics- Wiley Blackwell | | | |
| 1 | Bioinformatics for beginners - Supratim Choudhuri | | | 2 | Bioinformatics Volume-1 - Humana Press | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 9 | | 2 | 30 | | Practice | 12 | | 2 | 20 | | End-of-term exam | 16 | | 2 | 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 | 3 | 14 | 42 | | Sınıf dışı çalışma | 2 | 14 | 28 | | Arasınav için hazırlık | 3 | 8 | 24 | | Arasınav | 2 | 1 | 2 | | Uygulama | 1 | 14 | 14 | | Dönem sonu sınavı için hazırlık | 3 | 14 | 42 | | Dönem sonu sınavı | 2 | 1 | 2 | | Diğer 1 | 3 | 14 | 42 | | Diğer 2 | 2 | 14 | 28 | | Total work load | | | 224 |
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