C2135 Bioinformatics for practice

Faculty of Science
Spring 2023
Extent and Intensity
0/2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
Mgr. Lenka Malinovská, Ph.D. (lecturer)
Mgr. Josef Houser, Ph.D. (seminar tutor)
Guaranteed by
Mgr. Lenka Malinovská, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Supplier department: National Centre for Biomolecular Research - Faculty of Science
Timetable
Wed 16:00–17:50 B09/316
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 40 student(s).
Current registration and enrolment status: enrolled: 22/40, only registered: 0/40, only registered with preference (fields directly associated with the programme): 0/40
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should be able to: search for information and work with biological databases; perform independent bioinformatic analyses of data; prepare experimental project focused on protein cloning
Learning outcomes
At the end of the course students should: 1) Obtain basic knowledge of bioinformatics. Students should be able to: 1) Process bioinformational data. 2) Predict basic properties of biomacromolecules. 3) Utilize bioinformational tools for solving of biological problems.
Syllabus
  • Information search. General search, biological databases, resources for molecular biology information
  • Sequence alignment. Parameters (gaps, matrix). Nucleotide vs. amino acid alignments. Repetitions. Alignment as a tool for sequencing data analyses.
  • Gene prediction, prediction of proteins and their functions.
  • Primer design. Their importance, basic characteristics, secondary structure prediction, false priming, design of specific primers.
  • Cloning and restriction endonucleases digestion.
  • Protein properties prediction. Possibilities, comparison of demands and reliability of calculation and experiment.
  • Individual project: identification of putative genes in the genome of an unknown organism, which are important for pro virulence. Function prediction of encoded proteins.
  • Practical exercise 1. Polymerase chain reaction and agarose electrophoresis
  • Practical exercise 2. PCR product isolation, digestion using restriction endonucleases.
Literature
    recommended literature
  • ŠMARDA, Jan, Jiří DOŠKAŘ, Roman PANTŮČEK, Vladislava RŮŽIČKOVÁ and Jana KOPTÍKOVÁ. Metody molekulární biologie (Methods of molecular biology). 2. dotisk 1. vydání. Brno: Masarykova univerzita, 2010. 194 pp. ISBN 978-80-210-3841-7. info
  • XIONG, Jin. Essential bioinformatics. 1st pub. Cambridge: Cambridge University Press, 2006. xi, 339. ISBN 0521600820. info
Teaching methods
homework, practical exercises in silico, individual project
Assessment methods
own project finished, oral discussion
Language of instruction
Czech
Further Comments
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2011 - only for the accreditation, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/spring2023/C2135