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Course, academic year 2023/2024
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Bioinformatics for Biologists - MB160P44
Title: Bioinformatics for Biologists
Czech title: Bioinformatika pro biology
Guaranteed by: Department of Parasitology (31-161)
Faculty: Faculty of Science
Actual: from 2023
Semester: winter
E-Credits: 2
Examination process: winter s.:
Hours per week, examination: winter s.:1/0, Ex [TS]
Capacity: 20
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Explanation: do 2022/23 byl název Computational Genomics
Note: enabled for web enrollment
Guarantor: prof. RNDr. Jan Tachezy, Ph.D.
Teacher(s): doc. Mgr. Vladimír Hampl, Ph.D.
prof. RNDr. Jan Tachezy, Ph.D.
RNDr. Zdeněk Verner, Ph.D.
Mgr. Alois Zdrha
Annotation -
Program: Bioinformatics for Biologists
February 14-16 2024

Day 1:
Introduction to bioinformatics

Nucleotide and protein databases overview
NCBI, JGI, VEuPathDB etc.
Sequence formats, sequence visualization - Aliview
Sequence retrieval from databases
Keyword searches in NCBI
Retrieving sequences based on accession number
Downloading sequences from NCBI
BLAST
Types of blast: blasn, blastx, blastp, tblastn psi-blast
Blast parameters, taxonomic filtering
Sequence download from blast results

Lunch 12-13.00

Community annotation servers
ORCAE
VEuPathDB
Overview
Organism preferences
Personal Account
Retrieve window -upstream/downstream
Search strategy with multiple queries
Add user comments
Apollo sequence annotation

DAY 2:
DNA sequence analysis
Restriction enzyme analysis, Southern blot design
Codon usage analysis
Reverze translastion from protein to DNA
PCR primer design
qPCR Primer design, droplet digital Primer design
CRISPR Cas design
RNA secondary structure prediction

Lunch 12-13:00

Protein sequence analysis
Protein sorting/localization
TargetP, SignalP, POSORT, MitoProt...
Hydrophobicity plots
pI, net charge
Protein domain/motif analysis
Pfam, HHPRED, InterProScan
Structure prediction – Swiss Model
AlphaFold
Proteomic data analysis
Perseus, data incorporation, volcano plot analysis

Day 3:
Multiple sequence alignment
Theory about multiple sequence alignment
Alignment software, ClustalW MAFFT, Muscle
Manual investigation of multiple sequence alignments
Manual trimming
Automatic trimming methods: BMGE, TrimAl
Phylogenetic analysis
NJ tree using BioNJ
ML tree computation using Iq-Tree
Tree annotation in Figtree

Lunch 12.00-13.00

Exam

Last update: Tachezy Jan, prof. RNDr., Ph.D. (02.10.2023)
Literature - Czech

internetove odkazy dostanou studenti primo na kurzu

Last update: Kulíková Helena, RNDr. (24.04.2012)
Requirements to the exam - Czech

na konci kurzu test u pc ( realizace úkolu zadaneho pisemne pomoci PC a znalostí získaných v kurzu, vyhodnoceni ústní přímo se studentem na místě

Last update: Kulíková Helena, RNDr. (24.04.2012)
 
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