Study

Computing

Bioinformatics 1

  • Class 26
  • Practice 0
  • Independent work 0
Total 26

Course title

Bioinformatics 1

Lecture type

Elective

Course code

183492

Semester

6

ECTS

5

Course objectives

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.

Required reading

(.), 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

Minimal 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
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