Subjects

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Introduction to applied bioinformatics - GDXP09

Title:	Základy praktické bioinformatiky
Guaranteed by:	Department of Biochemical Sciences (16-16160)
Faculty:	Faculty of Pharmacy in Hradec Králové
Actual:	from 2019
Semester:	both
Points:	0
E-Credits:	0
Examination process:	oral
Hours per week, examination:	0/0, Ex [HT]
Capacity:	winter:unknown / unknown (unknown) summer:unknown / unknown (unknown)
Min. number of students:	unlimited
4EU+:	no
Virtual mobility / capacity:	no
Key competences:
State of the course:	taught
Language:	Czech
Teaching methods:	full-time
Level:
Note:	course is intended for doctoral students only you can enroll for the course in winter and in summer semester

Guarantor:	doc. Ing. Petra Matoušková, Ph.D.
Interchangeability :	GDPX09
Is interchangeable with:	GDPX09

Examination dates WS schedule SS schedule

Annotation -

Bioinformatics is an interdisciplinary field of science dealing with the storage, classification, analysis, and interpretation of biological data. In the subject Introduction to Applied Bioinformatics, students learn about possibilities of how to find and use bioinformatics databases and tools. This subject is focused mainly on practical usage and training of various web-based programs and software tools. Topics include scientific literature search, protein and nucleotide sequences databases, sequences comparison and their feature analysis, restriction analysis, primer design, specialized databases, etc.

Last update: Matoušková Petra, doc. Ing., Ph.D. (25.03.2025)

Course completion requirements -

Practical test by computer of practical knowledge of the subject with the possibility to use gained materials.

Last update: Matoušková Petra, doc. Ing., Ph.D. (25.03.2025)

Literature -

Recommended:

null. . In Selzer, Paul M. Marhöfer, Richard J., Koch, Oliver (eds.). Applied bioinformatics : an introduction . New York, NY: Springer Berlin Heidelberg, 2018, s. -. ISBN 978-3-319-68299-0..

Last update: Matoušková Petra, doc. Ing., Ph.D. (25.03.2025)

Syllabus -

1. Literature Search Options

UKAŽ, PubMed, Web of Science, Scopus

Citation management software (Web EndNote, EndNote, Mendeley)

Impact factor, H-index, predatory journals

2–4. Proteins

Protein databases and sequence search

Sequence formats and sequence manipulation

Sequence properties, domain prediction, and transmembrane region prediction

Sequence comparison: pairwise and multiple alignment, similarity search (BLAST), phylogenetic tree construction

5–9. Nucleic Acids

DNA sequence databases

Nucleotide sequence analysis: polymorphism detection, restriction analysis, in silico cloning

Primer design for various applications (qPCR, mutagenesis)

Gene search and identification, analysis of "unknown" sequences, open reading frame (ORF) identification

10. Specialized Databases

Expression Atlas, Enzyme, and others

Last update: Matoušková Petra, doc. Ing., Ph.D. (25.03.2025)