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