Course detail

Bioinformatics

FIT-IV108Acad. year: 2017/2018

An advanced course in bioinformatics (lecture and computer lab) building upon elementary mol.biology and/or bioinformatics courses.

Language of instruction

Czech

Mode of study

Not applicable.

Guarantor

Ing. Matej Lexa, Ph.D.

Department

Faculty of Informatics MU (FI MU)

Learning outcomes of the course unit

Item has no knowledges.

Prerequisites

There are no prerequisites

Co-requisites

Not applicable.

Planned learning activities and teaching methods

Not applicable.

Assesment methods and criteria linked to learning outcomes

Study evaluation is based on marks obtained for specified items. Minimimum number of marks to pass is 50.

Course curriculum

    Syllabus of lectures:
    1. Biological language (sequence segmentation, information-statistical analysis of biological sequences)
    2. Pattern matching (algoritms based on filtration and suffix arrays)
    3. Heuristic algorithms for similarity searching in biological sequences (BLAST, BLAT, Pattern Hunter)
    4. Regular expressions in bioinformatics
    5. Algorithms for analysis and prediction of structural data (secondary strukture, contacts inb proteins, domain identification)
    6. Algorithms for analysis and prediction of structural data (3D structure, structural comparisons)
    7. Working with molecular structures in Pymol
    8. New methods of DNA sequencing
    9. Genome assembly and other operations on short nucleic acid sequences
    10. Prediction of melting temperature in DNA and other nucleic acids (program mfold)
    11. RNA secondary structure
    12. DNA computing
    13. Comparative genomics of human (analysis of scientific papers)

Work placements

Not applicable.

Aims

Item has no goals.

Specification of controlled education, way of implementation and compensation for absences

There are no checked study.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

Not applicable.

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme CSE-PHD-4 Doctoral

    branch DVI4 , 0 year of study, winter semester, elective

Type of course unit

 

Lecture

13 hod., optionally

Teacher / Lecturer

Ing. Matej Lexa, Ph.D.

Syllabus

1. Biological language (sequence segmentation, information-statistical analysis of biological sequences)
2. Pattern matching (algoritms based on filtration and suffix arrays)
3. Heuristic algorithms for similarity searching in biological sequences (BLAST, BLAT, Pattern Hunter)
4. Regular expressions in bioinformatics
5. Algorithms for analysis and prediction of structural data (secondary strukture, contacts inb proteins, domain identification)
6. Algorithms for analysis and prediction of structural data (3D structure, structural comparisons)
7. Working with molecular structures in Pymol
8. New methods of DNA sequencing
9. Genome assembly and other operations on short nucleic acid sequences
10. Prediction of melting temperature in DNA and other nucleic acids (program mfold)
11. RNA secondary structure
12. DNA computing
13. Comparative genomics of human (analysis of scientific papers)

Fundamentals seminar

13 hod., optionally

Teacher / Lecturer

Ing. Matej Lexa, Ph.D.