Bioinformatics for Biologists - MB160P44
|
|
|
||
|
Last update: prof. RNDr. Jan Tachezy, Ph.D. (02.10.2023)
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: RNDr. Helena Kulíková (24.04.2012)
internetove odkazy dostanou studenti primo na kurzu |
|
||
|
Last update: RNDr. Helena Kulíková (24.04.2012)
na konci kurzu test u pc ( realizace úkolu zadaneho pisemne pomoci PC a znalostí získaných v kurzu, vyhodnoceni ústní přímo se studentem na místě |