SPIKES: Knowledge of the host-specific properties of the spike protein is of crucial importance to understand the adaptability of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to infect multiple species and alter transmissibility, particularly in humans. Here, we propose a spike protein predictor SPIKES incorporating with an inheritable bi-objective combinatorial genetic algorithm to identify the biochemical properties of spike proteins and determine their specificity to human hosts. We suggest that alterations of these amino acids between human and animal coronaviruses may provide insights into the development and transmission of SARS-CoV-2 in human and other species and support the discovery of targeted antiviral therapies.
FASTA format (e.g., example.fa)
git clone https://github.com/mingjutsai/SPIKES
cd SPIKESbuild AAIndex
cd src/aaindex
makebuild LIBSVM
cd src/libsvm_320
makecreate a new folder for the new analysis
mkdir example_outputperl SPIKES_main.pl example.fa example_outputresults of example.fa -> example_output/SPIKES_prediction_results.csv SPIKES_prediction_results.csv
- 1st: accession number of proteins
- 2nd: protein sequence
- 3rd: prediction score (normalized probabilities less than 0.5 are predicted to be human's Spike protein, those greater than 0.5 are predicted to be non-human's Spike protein.)
- All Human Spike protein sequences in FASTA format
- Prediction results of All Human Spike protein sequences
- All non-Human Spike protein sequences in FASTA format
- Prediction results of All non-Human Spike protein sequences
- SPIKES:Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2, STAR PROTOCOLS, 2022 [DOI:https://doi.org/10.1016/j.xpro.2022.101460]
- Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2. iScience, 2022 [PMID:34877480]
- Srinivasulu Yerukala Sathipati: sathipathi.srinivasulu@marshfieldclinic.org
- Ming-Ju Tsai: mingjutsai@hsl.harvard.edu