Course detail

Programming in Bioinformatics

FEKT-FPRGAcad. year: 2010/2011

The course is oriented to Perl programming in bioinformatics area. It studies introduction to programming language, it's syntax for DNA and protein sequence analysis and results interpretation.

Language of instruction

Czech

Number of ECTS credits

6

Mode of study

Not applicable.

Guarantor

doc. Ing. Jana Kolářová, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Learning outcomes of the course unit

Practical knowledge of Perl programming focused on work witk DNA and protein databases. Knowledge of basic DNA and protein sequence analysis and result interpetation.

Prerequisites

The subject knowledge on the Bachelor's degree level is requested.

Co-requisites

Not applicable.

Planned learning activities and teaching methods

Teaching methods depend on the type of the course unit as specified in the article 7 of BUT Rules for Studies and Examinations.

Assesment methods and criteria linked to learning outcomes

Requirements for completion of a course are specified by a regulation issued by the lecturer responsible for the course and updated for every year.

Course curriculum

Introduction to Perl programming. Data types, variables. Commands, operators, Regular expressions. Program components, functions, subfunctions. File input/output. Data structures. Text processing.

Work placements

Not applicable.

Aims

To acquire the basic programming skills in Perl. Selected solved problems for analysis of DNA and protein sequences will be studied. Introduction to types of data, how to operate and how to present results. Knowledge of proposal for program.

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

Limmitations of controlled teaching and its procedures are specified by a regulation issued by the lecturer responsible for the course and updated for every year.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

Moorhouse M, Barry P: Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice. Wiley; 1 edition, 2004. (EN)

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme BTBIO-F Master's

    branch F-BTB , 2. year of study, winter semester, compulsory

Type of course unit

 

Lecture

13 hours, optionally

Teacher / Lecturer

doc. Ing. Jana Kolářová, Ph.D.

Syllabus

1. Introduction to Perl programming, basic Unix commands.
2. Data types, variables.
3. Commands, operators, regular expressions.
4. Program components, functions, subfunctions.
5. File input/output.
6. Data structures.
7. Text processing.

Exercise in computer lab

39 hours, compulsory

Teacher / Lecturer

doc. Ing. Jana Kolářová, Ph.D.

Syllabus

1. Laboratory introduction and organization of laboratory works.
2. Introduction to CPAN client.
3. Directories, files, help.
4. Basic string matching.
5. DNA databases.
6. Bioinformatics tools.
7. BioPerl, basic objects.
8. DNA sequences.
9. Searching DNA sequence by BLAST.
10. Identification of specific sequences.
11. Presentation of student projects.
12. Presentation of student projects.
13. Final test.

The other activities

13 hours, compulsory

Teacher / Lecturer

doc. Ing. Jana Kolářová, Ph.D.

Syllabus

1. Study of DNA and proteins databases.
2. Study of searching algorithms.
3. Work on individual projects.