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Practical Training in Bioinformatics
Problem set
Project
Setup
Remote servers
Networks
Command line interface
Connecting to a remote server
R-Studio and Jupyter
ChatGPT
Checklist
Introduction to Unix
What is Unix?
Useful tricks for running commands
The file system
Navigation
Basic file operations
Looking at files
Search within files
Data wrangling
Transferring files between computers
Compressing and decompressing files
Checklist
In-class problems
Additional content
Good practices and reproducibility
Learning more about a command
Getting help online
Inputs and outputs
Combining commands
Writing and running scripts
Using software
Checklist
In-class problems
Additional content
Sequence data
Sequence data
Sequence databases
Searching the NCBI
Working in BioPython
Using Seq and SeqIO objects
Checklist
In-class problems
Additional content
Alignment
Comparative Sequence Analysis
BLAST
Using BLAST online
Searching for alignments
BLAST on the command line
Multiple sequence alignment (MSA)
Checklist
In-class problems
Additional content
Annotation
Gene prediction
Gene function
Gene function prediction
Automated annotation
Checklist
In-class problems
Additional content
Phylogenetics
Phylogenetic trees
Generating a phylogenetic tree via web-server
Collection and formatting of sequence data
Tree inference
Taxonomic classification
Checklist
In-class problems
Additional content
Protein structure data
Introduction to Structural Biology
The PDB repository and file format
Reading and manipulating structures in R
In-class problems
Protein interfaces and structural similarity
Protein pockets and interaction interfaces
Protein structural similarity
In-class problems
Predicting protein folding and the impact of mutations
Predicting protein structures using AlphaFold2
Structure based prediction of the impact of protein mutations
Prediction of the impact of protein mutations using FoldX
Structural bioinformatics - Project
Image analysis 1
What is ImageJ?
Images & pixels
Changing image appearance
Histograms
Types & bit-depths
Thresholding
In-class problems
Image analysis 2
The role of RGB
Image processing & analysis
Point operations
Point operations for single images
Filters
Image transforms
In-class problems
Ethics
Index