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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS CME 4425 INTRODUCTION TO BIOINFORMATICS ALGORITHMS ELECTIVE 2 2 0 6

Offered By

Computer Engineering

Level of Course Unit

First Cycle Programmes (Bachelor's Degree)

Course Coordinator

ASISTANT PROFESSOR ZERRIN IŞIK

Offered to

Computer Engineering

Course Objective

This course intends to equip students with basic knowledge and skills to solve computational poblems in the field of Bioinformatics.

Learning Outcomes of the Course Unit

1   Define Cell, DNA, RNA, Protein, Transcription and other basic biological concepts of bioinformatics 2   Use pairwise and multiple sequence alignment algorithms 3   Define PAM and BLOSUM Matrices, Dynamic Programming, 4   Define graph algorithms 5   Define learning algorithms for Bioinformatics

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Introduction to Cell, DNA, RNA, Protein, Evolution Computational Problems in Bioinformatics 2 Biological Relationships, PAM and BLOSUM Matrices 3 BLOSUM Matrices 4 Sequence Alignment 5 Dynamic Programming 6 Pairwise Sequence Alignment: BLAST Algorithm 7 Multiple Sequence Alignment 8 Midterm 1 9 Overview of Learning Algorithms for Bioinformatics 10 Probabilistic Models 11 Supervised Learning 12 Unsupervised Learning 13 Markov Models 14 Viterbi, Baum-Welch Algorithms

Recomended or Required Reading

Textbook: Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, The MIT Press, 2004 (ISBN-13: 978-0262101066) Supplemengtar Text: Introduction To Algorithms Third Edition, THOMAS H. CORMEN CHARLES E. LEISERSON RONALD L. RIVEST CLIFFORD STEIN, The MIT Press Massachusetts Institute of Technology Cambridge, 2001

Planned Learning Activities and Teaching Methods

1. Lectures 2. Individual and group work 3. Homeworks

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA 1 MTE MIDTERM EXAM 2 ASG ASSIGNMENT 3 FIN FINAL EXAM 4 FCG FINAL COURSE GRADE MTE * 0.25 + ASG * 0.25 + FIN * 0.50 5 RST RESIT 6 FCG FINAL COURSE GRADE MTE * 0.25 + ASG * 0.25 + RST * 0.50 *** Resit Exam is Not Administered in Institutions Where Resit is not Applicable.

Further Notes About Assessment Methods

None

Assessment Criteria

To be announced.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

zerrin@cs.deu.edu.tr

Office Hours

TBA

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Lectures 12 2 24 Tutorials 12 2 24 Preparations before/after weekly lectures 14 3 42 Preparation for midterm exam 2 8 16 Preparation for final exam 1 12 12 Preparing assignments 3 8 24 Final 1 2 2 Midterm 2 2 4 TOTAL WORKLOAD (hours) 148

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 PO.9 PO.10 LO.1 5 LO.2 5 4 3 LO.3 5 4 3 LO.4 5 4 3 LO.5 5 4 3