SubjectsSubjects(version: 901)
Course, academic year 2022/2023
  
Internet and bioinformatics - MC250P07B
Title: Internet a bioinformatika
Czech title: Internet a bioinformatika
Guaranteed by: Department of Biochemistry (31-250)
Faculty: Faculty of Science
Actual: from 2020
Semester: winter
E-Credits: 3
Examination process: winter s.:
Hours per week, examination: winter s.:2/1 Ex [hours/week]
Capacity: 19
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: Czech, English
Note: enabled for web enrollment
Guarantor: Mgr. Petr Jeřábek, Ph.D.
Teacher(s): Mgr. Petr Jeřábek, Ph.D.
doc. RNDr. Václav Martínek, Ph.D.
Opinion survey results   Examination dates   Schedule   
Annotation -
Last update: Mgr. Petr Jeřábek, Ph.D. (15.10.2020)
Subject of this course are internet databases and computational tools that are useful for biochemists. First, a short introduction to bioinformatics will be given. Introduction of the most important protein and DNA databases follows. Also basic tools of bioinformatics will be introduced, e.g. comparison of protein and DNA databases, searching for relative proteins, detection of key amino acids for proteins function. In the next part of this course, databases of macromolecular structures along with tools for their visualization will be discussed and exercised. Drawing chemical structures using ChemSketch software will be practiced as well. At the end, most important bibliographic databases and citation manager Zotero will be shown.

In case Erasmus students enroll in this course, lectures will be given in English.

The subject is lectured on-line using Zoom software https://cesnet.zoom.us/j/92896267436?pwd=bnZMbnNuWk5zTGpYY3I2QlBxZ05Udz09
Aim of the course -
Last update: HPTEST/NATUR.CUNI.CZ (23.11.2009)

The course is aimed to help students to be well oriented in Internet databases and to show where and how to mine reliable and relevant information.

Literature -
Last update: prof. RNDr. Petr Hodek, CSc. (09.09.2014)

Software manuals and on-line help are recommended study sources for the course. Handouts for lectures are not provided.

Requirements to the exam -
Last update: Mgr. Petr Jeřábek, Ph.D. (27.09.2019)

As their exams, students are going to solve practical tasks using computers. Students are allowed to use any source of information (personal notes, books, Google serch, ...).

Syllabus -
Last update: Mgr. Petr Jeřábek, Ph.D. (24.06.2019)

1.      Brief introduction to bioinformatics

2.      Protein and DNA databases (Uniprot, GenBank, e.g.)

3.      Basic bioinformatics tools (BLAST, pairwise and multiple sequence alignment analysis with Jalview software)

4.      Structural databases (Protein Data Bank, e.g.)

5.      Vizualization of biomolecules using PyMol software

6.      Drawing chemical structures using ChemSketch software

7.      Bibliographic databases (PubMed, Web of Science) and other information resources

8.      Citation manager Zotero

 
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