Course Unit Code | Course Unit Title | Type of Course Unit | Year of Study | Semester | Number of ECTS Credits | TBT-23-127 | BİTKİ ISLAHINDA BİLGİSAYAR PROGRAMLARI: FİLOGENETİK VE KÜMELEME ANALİZLERİ | Elective | 1 | 3 | 6 |
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Level of Course Unit |
Third Cycle |
Objectives of the Course |
To teach the methods of phylogenetic analysis using bioinformatics programs and interpretation of the obtained results, to examine population structures and to make clustering analysis. |
Name of Lecturer(s) |
Dr. Fatih DEMİREL |
Learning Outcomes |
1 | Ability to develop and deepen knowledge in the same or different field at the level of expertise based on undergraduate qualifications | 2 | An ability to comprehend the interaction between disciplines related to the field | 3 | An ability to use theoretical and practical knowledge at an expert level | 4 | To be able to create new information by integrating the information in the field with the information coming from different disciplines; ability to solve problems requiring expertise by using scientific research methods | 5 | Ability to construct a problem in his / her field independently, develop a solution method, solve it, evaluate the results and apply when necessary | 6 | Ability to develop new strategic approaches and to produce solutions by taking responsibility in unforeseen complex situations in the field of applications | 7 | Ability to critically evaluate the information related to the field, to direct learning and the ability to conduct advanced studies independently | 8 | Ability to transfer the current developments in the field and his / her studies to the groups within and outside the field systematically in written, oral and visual form. | 9 | Ability to critically examine social relations and the norms directing these relations, and to develop and change them when necessary | 10 | Ability to communicate in oral and written in at least one foreign language | 11 | Ability to develop strategies, policies and implementation plans in the field and evaluate the results within the framework of quality processes | 12 | Ability to teach and control these values by considering social, scientific and ethical values in the stages of data collection, interpretation and announcement |
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Mode of Delivery |
Daytime Class |
Prerequisites and co-requisities |
none |
Recommended Optional Programme Components |
Morphological markers and their scoring, DNA markers and their scoring, Entering the data to the computer, Use of PAUP program, Use of bioinformatics programs, Determination of genetic proximity and distance between plant species, varieties and genotypes, To be able to use and interpret the methods of parsimony and genetic distance. |
Course Contents |
Master and Ph.D. students who have successfully completed this course will have the following qualifications;
1) They know DNA markers and their evaluation
2) They know packet programs related to phylogenetic analysis
3) They know parsimony analysis
4) They know UPGMA and Neighbor joining methods
5) They know how to obtain pedigree and interpretation of results |
Weekly Detailed Course Contents |
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1 | Morphological markers and scoring | none | none | 2 | Molecular markers and scoring | | | 3 | Entering data on the computer | | | 4 | Using the NTsysPc program | | | 5 | Basic components analysis with NTsysPc program | | | 6 | Use of PAUP program | | | 7 | Use of PHYLIP program | | | 8 | Neighbor Joining and Upgma Analysis | | | 9 | Obtaining Genealogy, Interpretation and Presentation of Results | | | 10 | STRUCTURE program use | | | 11 | The population of the structure resulting Approval, Interpretation and presentation of results. | | | 12 | Determination of Genetic Proximity and Distance Between Plant Species, Varieties and Genotypes | | | 13 | Parsimony Analysis and Genetic Distance Method | | | 14 | Interpretation and Presentation of Clustering Data . | | |
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Recommended or Required Reading |
Molecular Markers in Plant Genetics and Biotechnology (D. Vienne)
Molecular Evoılution and Phylogenetics (M. Nei and S. Kumar)
Phylogenetic Trees Made Easy (B.G. Hall) |
Planned Learning Activities and Teaching Methods |
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Assessment Methods and Criteria | |
Midterm Examination | 1 | 100 | SUM | 100 | |
Final Examination | 1 | 100 | SUM | 100 | Term (or Year) Learning Activities | 50 | End Of Term (or Year) Learning Activities | 50 | SUM | 100 |
| Language of Instruction | Turkish | Work Placement(s) | none |
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Workload Calculation |
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Attending Lectures | 14 | 3 | 42 |
Brain Storming | 14 | 3 | 42 |
Writing Paper | 2 | 3 | 6 |
Self Study | 14 | 3 | 42 |
Homework | 14 | 3 | 42 |
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Contribution of Learning Outcomes to Programme Outcomes |
LO1 | 5 | | | | | | | LO2 | 5 | | | | | | | LO3 | | 5 | | | | | | LO4 | | | 5 | | | | | LO5 | | | | 5 | | | | LO6 | | | | | 5 | | | LO7 | | | | | | 5 | | LO8 | | | | | | | 5 | LO9 | 5 | | | | | | 5 | LO10 | | | | | | 5 | | LO11 | | | | | 5 | | | LO12 | | 5 | 4 | 4 | | | |
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* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High |
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Iğdır University, Iğdır / TURKEY • Tel (pbx): +90 476
226 13 14 • e-mail: info@igdir.edu.tr
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