A sequence alignnment and analysis ofSARS-CoV-2 spike glycoprotein
Preamble
Coronavirus glycoprotein
1
Introduction
1.1
Learning goals
1.2
Exercise files
1.3
Software used during this tutorial
1.3.1
A note about Docker
1.4
Style
2
Getting started
2.1
Get Sequences
2.2
Getting organized
2.3
Checking sequences
3
Complete sequences dataset
3.1
Removing partial and sequences with
X
3.2
Counting sequences
3.3
Evaluating sequence length
4
Sequence alignment
4.1
Run clustal omega
4.2
Alignment format
4.3
Consensus sequence
5
Distance matrix
5.1
Convert to number of differences matrix
5.2
Find largest value in matrix
5.3
Alternatives
6
Align related sequences
6.1
Spike protein features
6.2
Related sequences
6.3
Create the alignment
6.3.1
Step 1: download sequence files
6.3.2
Step 2: download structure files
6.3.3
Step 3: create alignment
6.3.4
Results
7
Alignment Results
7.1
Color alignment
7.1.1
Remove PDB sequences (optional)
7.1.2
Create colored output
7.2
Furin site
7.3
Alignment conclusion
8
Acknowledgments
8.1
Licensed icons used:
8.2
This document
Appendix
A
Full sequence alignments
B
PyMOL scripts
C
About the Author
References
Published with bookdown
A sequence alignment and analysis of SARS-CoV-2 spike glycoprotein
Chapter 8
Acknowledgments