June 26, 2020.
I have added a new entry under the “Tutorials” menu for “bioinformatics” to provide a place for tutorials that are more than just about one subject. “bioinformatics is the science of collecting and analyzing complex biochemical and biological information using computers.” It may provide the tools to “look under the hood” of life, that is why I selected this image illustration.
The first entry is about the SARS-CoV-2 that causes the Covid19 disease pandemic at the moment. It is meant to learn about the sequence of the spike glycoprotein that the virus uses to enter cells. The spike protein was the subject of a PyMOL tutorial a couple months ago (Blog entry Covid-19 Coloring Book and PyMOL scripts book) to learn about its structure and about. making PyMOL scripts.
The new tutorial (SARS-COV-2-Spike-Alignment) is about the spike protein sequence and its alignment with similar sequences from other closely related SARS coronaviruses and learning about the processes involved from sequence retrieval from NCBI to multiple sequence alignment with
clustal omega and
The tutorial is also about using the very useful Unix utilities to help in the process without doing any programming per se.
The tutorial uses a lot of the Unix “tricks” that I use all the time. They might not satisfy a purist computer scientist, but they certainly have the spirit of getting things done. I find it amazing that these utilities are so powerful even if some of them have been devised decades ago.
Spike alignment background image composite: SARS-CoV-2 “model” created with CellPaint (Scripps.) Overlay are PyMOL renderings of spike protein (PDB 6VXX.) (Left: close view of a mature alium flower pistils that look-alike the protein spike – JYS photo taken today, June 26, 2020.)