Subjects

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Introduction to applied bioinformatics - GDEXP09

Title:	Introduction to applied bioinformatics
Guaranteed by:	Department of Biochemical Sciences (16-16160)
Faculty:	Faculty of Pharmacy in Hradec Králové
Actual:	from 2020
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:	English
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 :	GDEPX09
Is interchangeable with:	GDEPX09

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 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, databases of protein and nucleotide sequences, 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 -

To obtain course credit, students must meet the attendance requirement (at least 80%) and complete and submit all short exercises (homework) covered in the seminars (submission via Moodle).

The exam is conducted in written form on computers by completing a given set of tasks (with the possibility of using all available materials).

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

Literature

Selzer, Paul M. Applied bioinformatics : an introduction. Springer, 2018. 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)