Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
TBT-23-127BİTKİ ISLAHINDA BİLGİSAYAR PROGRAMLARI: FİLOGENETİK VE KÜMELEME ANALİZLERİElective136
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
1Ability to develop and deepen knowledge in the same or different field at the level of expertise based on undergraduate qualifications
2An ability to comprehend the interaction between disciplines related to the field
3An ability to use theoretical and practical knowledge at an expert level
4To 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
5Ability to construct a problem in his / her field independently, develop a solution method, solve it, evaluate the results and apply when necessary
6Ability to develop new strategic approaches and to produce solutions by taking responsibility in unforeseen complex situations in the field of applications
7Ability to critically evaluate the information related to the field, to direct learning and the ability to conduct advanced studies independently
8Ability 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.
9Ability to critically examine social relations and the norms directing these relations, and to develop and change them when necessary
10Ability to communicate in oral and written in at least one foreign language
11Ability to develop strategies, policies and implementation plans in the field and evaluate the results within the framework of quality processes
12Ability to teach and control these values by considering social, scientific and ethical values in the stages of data collection, interpretation and announcement
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
WeekTheoreticalPracticeLaboratory
1Morphological markers and scoringnonenone
2Molecular markers and scoring
3Entering data on the computer
4Using the NTsysPc program
5Basic components analysis with NTsysPc program
6Use of PAUP program
7Use of PHYLIP program
8Neighbor Joining and Upgma Analysis
9Obtaining Genealogy, Interpretation and Presentation of Results
10STRUCTURE program use
11The population of the structure resulting Approval, Interpretation and presentation of results.
12Determination of Genetic Proximity and Distance Between Plant Species, Varieties and Genotypes
13Parsimony Analysis and Genetic Distance Method
14Interpretation and Presentation of Clustering Data .
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
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
Midterm Examination1100
SUM100
End Of Term (or Year) Learning ActivitiesQuantityWeight
Final Examination1100
SUM100
Term (or Year) Learning Activities50
End Of Term (or Year) Learning Activities50
SUM100
Language of Instruction
Turkish
Work Placement(s)
none
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Attending Lectures14342
Brain Storming14342
Writing Paper236
Self Study14342
Homework14342
TOTAL WORKLOAD (hours)174
Contribution of Learning Outcomes to Programme Outcomes
PO
1
PO
2
PO
3
PO
4
PO
5
PO
6
PO
7
LO15      
LO25      
LO3 5     
LO4  5    
LO5   5   
LO6    5  
LO7     5 
LO8      5
LO95     5
LO10     5 
LO11    5  
LO12 544   
* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High
 
Iğdır University, Iğdır / TURKEY • Tel (pbx): +90 476 226 13 14 • e-mail: info@igdir.edu.tr