SubjectsSubjects(version: 873)
Course, academic year 2020/2021
Introduction into bioinformatics - MB130C52
Title: Úvod do bioinformatiky
Czech title: Úvod do bioinformatiky
Guaranteed by: Department of Experimental Plant Biology (31-130)
Faculty: Faculty of Science
Actual: from 2019
Semester: winter
E-Credits: 2
Examination process: winter s.:
Hours per week, examination: winter s.:0/2 C [hours/week]
Capacity: 36
Min. number of students: 5
State of the course: taught
Language: Czech
Explanation: V případě, že je kurs plný, doporučuji zapsat MB130C52E.
Additional information:
Guarantor: doc. RNDr. Fatima Cvrčková, Dr.
Teacher(s): Mgr. Radek Bezvoda, Ph.D.
doc. RNDr. Fatima Cvrčková, Dr.
Attributes: Modul Ostatní předměty
Incompatibility : MB130C52E
N//Is incompatible with: MB130C52E
Opinion survey results   Examination dates   Schedule   
Annotation -
Last update: VOTRUB (10.02.2003)
The course aims towards acquisition of basic skills required for searching and analysis of biological sequence data with the aid of commonly available (web-based or freely downloadable) tools.

Literature - Czech
Last update: FATIMA (14.03.2007)

Cvrčková, F.: Úvod do praktické bioinformatiky. Academia, Praha 2006.

Requirements to the exam - Czech
Last update: doc. RNDr. Fatima Cvrčková, Dr. (04.11.2011)

Předložení výsledků řešených vybraných příkladů dle specifikace na webových stránkách kursu včetně odpovědi na kontrolní otázky.

Syllabus -
Last update: VOTRUB (03.02.2003)

1. Orientation in data resources: sequence databases, searching, downloading. Genome sites and other "added value" resources. Tools for data access and manipulation.

2. Basic handling of sequence data. Identification of relevant sequence portions, file formats, reformatting utilities. Restriction site analysis and translation of DNA sequences.

3. Sequence similarity searches. Methods - BLAST, FASTA. Theoretical principles. Scoring matrices (PAM, BLOSUM). Special implementations of BLAST.

4. Motif searches and domain structure analysis. SMART, PROSITE and similar resources. Searching for specific signals (protein - localisation and degradation, DNA - binding sites). Pattern searches, pattern development.

5. Gene identification and gene building: algorithmic searching for coding sequences and intron/exon structures in chromosomal DNA.

6. Construction and interpretation of sequence alignments. Automated vs. manual methods (CLUSTAL vs. MACAW). Use of EST alignments for verifying gene structure predictions. Construction of protein sequence alignments and derived sequence patterns or profiles.

7. Phylogenetic trees: construction and critical interpretation. Problem of meaningful data selection. The PHYLIP package and its use.

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