COURSE UNIT TITLE

: INTRODUCTION TO BIOINFORMATICS

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
CHE 4232 INTRODUCTION TO BIOINFORMATICS ELECTIVE 2 0 0 4

Offered By

Chemistry

Level of Course Unit

First Cycle Programmes (Bachelor's Degree)

Course Coordinator

PROFESSOR DOCTOR LEVENT ÇAVAŞ

Offered to

Chemistry (Evening)
Chemistry

Course Objective

Bioinformatics is a newly founded multidisciplinary field. It consists of biological databases and computational sciences. During this course, the students will learn fundamental concepts of bioinformatics such as protein-DNA databases, several web-based bioinformatics tools developed for protein parameters, multiple sequence analysis, gen
finding within a whole genome, motif extraction, membrane helices, intrinsically unfolded regions in proteins and phylogenetic trees.

Learning Outcomes of the Course Unit

1   The students will be able to find FASTA sequences of protein and DNA from related databanks
2   The students will be able to apply suitable bioinformatics tools to analyse multiple sequence analysis, unfolded regions and protein parameters.
3   The students will be able to predict membrane helices, to visualise enzyme active regions and receptor ligand interactions.
4   The students will be able to estimate motifs in protein sequence and to construct phylogenetic analysis.

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Introduction to Bioinformatics
2 Protein Data Banks-1 (Uniprot, expasy)
3 Protein Data Banks-2 (RSCB-Protein Data Bank)
4 DNA Data Banks-1
5 DNA Data Banks-2
6 In silico protein parameters analysis
7 Intrinsically unfolded regions in proteins
8 General Revision
9 Prediction of membrane helices in membrane proteins
10 3D Enzyme active site screening (YASARA)
11 Receptor-Ligand interactions (Auto Dock Vina)
12 Constructions of phylogenetic trees, motif extraction tools
13 Student assignment project presentations
14 Student assignment project presentations

Recomended or Required Reading

Lesk, A., (2006). Introduction to Bioinformatics, Oxford University Pres, New York
Various Internet Sources on Bioinformatics:
http://www.expasy.ch
http://www.ebi.ac.uk
http://www.rcsb.org

Planned Learning Activities and Teaching Methods

Presentation
Questions and answers
Homework
Application

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA
1 MTE MIDTERM EXAM
2 ASG ASSIGNMENT
3 FIN FINAL EXAM
4 FCGR FINAL COURSE GRADE (RESIT) MTE * 0.25 + ASG * 0.35 + FIN * 0.40
5 RST RESIT
6 FCGR FINAL COURSE GRADE (RESIT) MTE * 0.25 + ASG * 0.35 + RST * 0.40


Further Notes About Assessment Methods

None

Assessment Criteria

The learning of fundamental concepts given in the lectures, associating of concepts, constracting relationship between cause and effect, interpreting on the questions through current knowledge, and evaluation of idea production will be carried out by mid terms, final exam, active participation to the lecture, home works

Language of Instruction

English

Course Policies and Rules

The course policies and rules can be found from web site of Faculty of Science (www.deu.edu.tr)

Contact Details for the Lecturer(s)

Levent CAVAS, Dokuz Eylul University,Faculty of Science, Department of Chemistry
Division of Biochemistry, 35390, Kaynaklar Campus, IZMIR-TURKEY
Tel: +90 232 3018701 (office)
Email: lcavas@deu.edu.tr

Office Hours

Wednesday 16:40-17:00

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 14 2 28
Preparations before/after weekly lectures 11 1 11
Preparation for midterm exam 1 15 15
Preparation for final exam 1 15 15
Preparing presentations 1 30 30
Midterm 1 2 2
Final 1 2 2
TOTAL WORKLOAD (hours) 103

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8PO.9PO.10PO.11PO.12PO.13PO.14PO.15PO.16PO.17
LO.15341553355555
LO.25441553355555
LO.35341553355555
LO.45344553355555

CONTACT INFORMATION
Dokuz Eylül Üniversitesi Cumhuriyet Bulvarı No: 144 35210 Alsancak / İZMİR
Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

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