INTERNATIONAL BURCH UNIVERSITY
Faculty of Engineering and Natural Sciences
Department of Genetics and Bioengineering
2014-2015

SYLLABUS
Code Name Level Year Semester
GBE 307 Bionformatics Undergraduate 3 Fall
Status Number of ECTS Credits Class Hours Per Week Total Hours Per Semester Language
Compulsory 5 2 + 2 130 English

Instructor Assistant Coordinator
Şenol Doğan, Assist. Prof. Dr. Şenol Doğan Şenol Doğan, Assist. Prof. Dr.
[email protected] [email protected] no email

COURSE OBJECTIVE
This course is designed to show the importance of bioinformatics as a method to overcome modern biomedical research problems and to enable skill development in software using, critical evaluation of the results and their interpretation.Another main objective of this course will be to introduce students to the fundamentals of molecular biology and computer science. These principals underlie much of modern bioinformatics, and students will be shown how they apply to many of the basic predictive methods that are of common use in the field. This course also aims to provide students with a practical and hands-on experience with common bioinformatics tools and databases. Students will be trained in the basic theory and application of programs used for database searching, protein and DNA sequence analysis, prediction of protein function, and building phylogenetic trees. Specific types of analysis discussed in the course will include but is not limited to: Detection of homology with BLAST, prediction of transmembrane segments, multiple alignment of sequences, prediction of protein domains, prediction of protein localization, and building phylogenetic trees.

COURSE CONTENT
Week
Topic
  1. Origin & History of Bioinformatics
  2. Biology in the Computer Age
  3. Biological Databases
  4. Bioinformatics: Programs, Tools, Projects, Applications
  5. Using Nucleotide Sequence Databases
  6. Using Protein and Specialized Sequence Databases
  7. Working with a Single DNA Sequence
  8. Midterm
  9. Working with a Single Protein Sequence
  10. Similarity Searches on Sequence Databases
  11. Building a Multiple Sequence Alignment
  12. Editing and Publishing Alignments
  13. Working with Protein 3-D Structures
  14. Working with RNA
  15. Building Phylogenetic Trees

LABORATORY/PRACTICE PLAN
Week
Topic
  1. Searching articles

  1. Finding genomic view, physical and genetical map
  2. Blast types and blast of a gene
  3. USCS Genome finder tool
  4. TAIR, for plant genome
  5. Uniprot, protein blast and alignment
  6. Primer Design
  7. Midterm
  8. Finding different phylogenetic tree tools and applying our gene
  9. Micro RNA finder tools
  10. Ensembl exon coding, alternative splicing products
  11. TCGA web tool
  12. Genecards tool
  13. OMIM, inherited disease
  14. Presentations of students

TEACHING/ASSESSMENT
Description
  • Lectures
  • Presentation
  • Seminar
  • Self Evaluation
  • Project
  • Assignments
Description (%)
Method Quantity Percentage (%)
Project10
Midterm Exam(s)40
Final Exam150
Total: 100
Learning outcomes
  • Actively participate in courses and begin to take responsibility for learning
  • Begin to work effectively as part of a team, developing interpersonal, organisational and problem-solving skills within a managed environment, exercising some personal responsibility.
  • Present information in oral, written or graphic forms in order to communicate effectively with peers and tutors.
  • Search genetics data from webtools and analyze them
TEXTBOOK(S)
  • 1) Introduction to Bioinformatics, Arthur Lesk, 3rd Edition, Oxford Bioinformatics for Dummies, Last Edition
  • 2)Bioinformatics for Geneticist, Michael R. Barnes, Wiley 2007

ECTS (Allocated based on student) WORKLOAD
Activities Quantity Duration (Hour) Total Work Load
Lecture (14 weeks x Lecture hours per week)21428
Laboratory / Practice (14 weeks x Laboratory/Practice hours per week)21428
Midterm Examination (1 week)122
Final Examination(1 week)122
Preparation for Midterm Examination12020
Preparation for Final Examination12020
Assignment / Homework/ Project13030
Seminar / Presentation 0
Total Workload: 130
ECTS Credit (Total workload/25): 5