Bioinformatics 1
Learning Outcomes
- Explain some of the issues and challenges in contemporary bioinformatics
- Evaluate bioinformatics algortihms
- Design algorithms solving sequence assembly problems
- Compare and evalute methods for sequence alignment
- Design algorithms for building phylogenetics trees
- Analyze data from biological databases
- Design index structures based on suffix trees and suffix arrays
Forms of Teaching
Lectures
Lectures in the classroom
Independent assignmentsTeam work on the implementation of a method.
Grading Method
Continuous Assessment | Exam | |||||
---|---|---|---|---|---|---|
Type | Threshold | Percent of Grade | Threshold | Percent of Grade | ||
Seminar/Project | 0 % | 40 % | 0 % | 40 % | ||
Mid Term Exam: Written | 40 % | 25 % | 0 % | |||
Final Exam: Written | 40 % | 35 % | ||||
Exam: Written | 40 % | 60 % |
Week by Week Schedule
- Protein, RNA and DNA; Bioinformatics databases; Data formats.
- Biological sequences and structures; Dynamic programming algorithms; Project.
- Dynamic programming algorithms; Project.
- Suffix trees; Project.
- Suffix trees; Project.
- Suffix arrays; Project.
- Suffix arrays; FM index; Project.
- Midterm exam.
- Multiple sequence alignment; Database search; Basic Local Alignment Search Tool (BLAST) algorithm.
- Alignment; Substitution model; Project.
- Tree building; Tree evaluation; Project.
- Sequencing methods; Read mapping; Project.
- De novo assembly; Overlap-Layout-Consensus; Project.
- String graph; De Bruijn graph; Project.
- Final exam.
Study Programmes
University undergraduate
Computing (study)
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(6. semester)
Electrical Engineering and Information Technology (study)
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(6. semester)
University graduate
Audio Technologies and Electroacoustics (profile)
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(2. semester)
Computational Modelling in Engineering (profile)
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(2. semester)
Computer Engineering (profile)
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(2. semester)
Specialization Course
(2. semester)
Control Systems and Robotics (profile)
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(2. semester)
Data Science (profile)
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(2. semester)
Electrical Power Engineering (profile)
Elective course
(2. semester)
Electric Machines, Drives and Automation (profile)
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Electronic and Computer Engineering (profile)
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Electronics (profile)
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(2. semester)
Information and Communication Engineering (profile)
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(2. semester)
Information Processing (profile)
Specialization Course
(2. semester)
Software Engineering and Information Systems (profile)
Elective Courses
(2. semester)
Specialization Course
(2. semester)
Literature
(.), Mile Sikic, Mirjana Domazet-Loso, Skripta iz bioinformatike,
(.), N.C. Jones, P. J. Pevzner, An Introduction to Bioinformatics Algorithms,
(.), D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology,
Associate Lecturers
For students
General
ID 183492
Summer semester
5 ECTS
L1 English Level
L1 e-Learning
30 Lectures
0 Exercises
5 Laboratory exercises
0 Project laboratory
Grading System
90 Excellent
75 Very Good
60 Good
50 Acceptable