STAR Protocols
Volume 3, Issue 3, 16 September 2022, 101460
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Protocol
SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

https://doi.org/10.1016/j.xpro.2022.101460Get rights and content
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Highlights

  • Identify informative physicochemical properties of the SARS-CoV-2 spike protein

  • SPIKES predicts the species specificity across diverse host species of SARS-CoV-2

  • This protocol addresses spike protein sequence retrieval and analysis procedures

  • Differences exist in the S protein properties of diverse host species CoVs

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Summary

We describe a protocol to identify physicochemical properties using amino acid sequences of spike (S) proteins of SARS-CoV-2. We present an S protein prediction technique named SPIKES, incorporating an inheritable bi-objective combinatorial genetic algorithm to determine the host species specificity. This protocol addresses the S protein amino acid sequence data collection, preprocessing, methodology, and analysis.

For complete details on the use and execution of this protocol, please refer to Yerukala Sathipati et al. (2022).

Subject areas

Bioinformatics
Microbiology
Proteomics
Systems biology

Data and code availability

The protein sequence data used in this analysis is available at https://www.gisaid.org and https://www.ncbi.nlm.nih.gov.

The pipeline of SPIKES and prediction model files are available at https://github.com/mingjutsai/SPIKES; https://doi.org/10.5281/zenodo.6502505.

https://doi.org/10.17632/6s9wt7zzxz.1.

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