Bioinformatics 1

Data is displayed for academic year: 2023./2024.

Lecturers

Prof.
Mile Šikić
Assoc. Prof.
Mirjana Domazet-Lošo

Lectures

Asst. Prof.
Krešimir Križanović

Course Description

In the last two decades, bioinformatics has expanded rapidly as the discipline that narrowly connects biology with computer science. The accelerating growth of biological data collection has inspired development of new computational methods for storage, retrieval, analysis and visualization of such data. This course will focus on the computational aspects of biological sequence analysis. Lectures will cover algorithms and tools developed for pairwise and multiple sequence alignment, genome and transcriptome assembly, gene finding and phylogenetic tree reconstruction.

Study Programmes

University undergraduate
[FER3-EN] Computing - study
Elective Courses (6. semester)
[FER3-EN] Electrical Engineering and Information Technology - study
Elective Courses (6. semester)
University graduate
[FER3-EN] Data Science - profile
Recommended elective courses (2. semester)

Learning Outcomes

  1. Explain some of the issues and challenges in contemporary bioinformatics
  2. Evaluate bioinformatics algortihms
  3. Design algorithms solving sequence assembly problems
  4. Compare and evalute methods for sequence alignment
  5. Design algorithms for building phylogenetics trees
  6. Analyze data from biological databases
  7. Design index structures based on suffix trees and suffix arrays

Forms of Teaching

Lectures

Lectures in the classroom

Independent assignments

Team 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 0 % 25 % 0 %
Final Exam: Written 40 % 35 %
Exam: Written 40 % 60 %

Week by Week Schedule

  1. Protein, RNA and DNA, Bioinformatics databases, Data formats
  2. Biological sequences and structures, Dynamic programming algorithms, Project
  3. Dynamic programming algorithms, Project
  4. Suffix trees, Project
  5. Suffix trees, Project
  6. Suffix arrays, Project
  7. Suffix arrays, FM index, Project
  8. Midterm exam
  9. Multiple sequence alignment, Database search, Basic Local Alignment Search Tool (BLAST) algorithm
  10. Alignment, Substitution model, Project
  11. Tree building, Tree evaluation, Project
  12. Sequencing methods, Read mapping, Project
  13. De novo assembly, Overlap-Layout-Consensus, Project
  14. String graph, De Bruijn graph, Project
  15. Final exam

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,

For students

General

ID 223333
  Summer semester
5 ECTS
L1 English Level
L1 e-Learning
30 Lectures
0 Seminar
0 Exercises
5 Laboratory exercises
0 Project laboratory
0 Physical education excercises

Grading System

90 Excellent
75 Very Good
60 Good
50 Sufficient

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