Bioinformatics for Biologists - MB160P44
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Probíhá turnusově pře začátkem letního semestru (14.16.2. 2024). Počet studentů omezen na
20. Program: Bioinformatics for Biologists 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 Odborná literatura: Informace na internetu Poslední úprava: Tachezy Jan, prof. RNDr., Ph.D. (02.10.2023)
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internetove odkazy dostanou studenti primo na kurzu Poslední úprava: Kulíková Helena, RNDr. (24.04.2012)
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na konci kurzu test u pc ( realizace úkolu zadaneho pisemne pomoci PC a znalostí získaných v kurzu, vyhodnoceni ústní přímo se studentem na místě Poslední úprava: Kulíková Helena, RNDr. (24.04.2012)
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