Hi, everyone. So I’ve been assigned the task of evaluating effects that certain SNPs would have on some viral proteins. I’m a complete noob in bioinformatics, so where should I begin?
Basically, I need to compare mutant AA sequences with wild types and infer changes in their functions caused by changes in the primary sequence. Some of those proteins have been described pretty well and even have PDBs, but others are barely mentioned anywhere.
Also, I have access to a pretty capable cluster that runs Bash, so both program packages and UI programs are welcome. Thanks!
You can start with BLASTp
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
For multiple sequence alignment use Muscle, MAAFT.
https://www.ebi.ac.uk/Tools/msa/muscle/
https://www.ebi.ac.uk/Tools/msa/mafft/
Also you can find out multiple features of protein using one of my team work:
https://webs.iiitd.edu.in/raghava/pfeature/
you can use these features in machine learning modelling.
You can also make classification and regression model using
https://webs.iiitd.edu.in/raghava/pfeature/model_classif.php
https://webs.iiitd.edu.in/raghava/pfeature/model_reg.php
I hope it would help you.
All the best.
Maybe this can help: https://predictprotein.org/
Also this paper may be of interest:
Article Scoring amino acid mutation to predict pandemic risk of avia...
Best wishes,
R.
http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
https://cluspro.bu.edu/home.php
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