SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

Srinivasulu Yerukala Sathipati; Ming Ju Tsai; Tonia Carter; Sanjay K. Shukla; Shinn Ying Ho

doi:10.1016/j.xpro.2022.101460

SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

Srinivasulu Yerukala Sathipati^*, Ming Ju Tsai, Tonia Carter, Sanjay K. Shukla, Shinn Ying Ho

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

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).

Original language	English
Article number	101460
Journal	STAR Protocols
Volume	3
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2022.101460
State	Published - 16 Sep 2022

Keywords

Bioinformatics
Microbiology
Proteomics
Systems biology

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10.1016/j.xpro.2022.101460

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title = "SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2",

abstract = "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).",

keywords = "Bioinformatics, Microbiology, Proteomics, Systems biology",

author = "{Yerukala Sathipati}, Srinivasulu and Tsai, {Ming Ju} and Tonia Carter and Shukla, {Sanjay K.} and Ho, {Shinn Ying}",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s)",

year = "2022",

month = sep,

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doi = "10.1016/j.xpro.2022.101460",

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T2 - Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

AU - Yerukala Sathipati, Srinivasulu

AU - Tsai, Ming Ju

AU - Carter, Tonia

AU - Shukla, Sanjay K.

AU - Ho, Shinn Ying

PY - 2022/9/16

Y1 - 2022/9/16

N2 - 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).

AB - 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).

KW - Bioinformatics

KW - Microbiology

KW - Proteomics

KW - Systems biology

UR - http://www.scopus.com/inward/record.url?scp=85131966650&partnerID=8YFLogxK

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DO - 10.1016/j.xpro.2022.101460

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AN - SCOPUS:85131966650

SN - 2666-1667

VL - 3

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 101460

ER -

SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2

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Keywords

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