Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach

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1. Version published to 10.1016/j.meegid.2020.104389

   Oct 1, 2020
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.04.07.030924: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   For multiple sequence alignment (MSA), Genome Detective Coronavirus Typing Tool uses a reference dataset of 431 whole genome sequences (WGS) where 386 WGS were from known nine coronavirus species.	WGS suggested: None
   The dataset was then aligned with MUSCLE [24].	MUSCLE suggested: (MUSCLE, RRID:SCR_011812)
   Entropy (H(x)) plot of nucleotide variations in SARS-CoV-2 genome was constructed using BioEdit [25].	BioEdit suggested: (BioEdit, RRID:SCR_007361)
   MEGA X (version 10.1.7) was used to construct the MSAs and the phylogenetic tree using pairwise alignment and neighbor-joining methods in ClustalW …

   SciScore for 10.1101/2020.04.07.030924: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   For multiple sequence alignment (MSA), Genome Detective Coronavirus Typing Tool uses a reference dataset of 431 whole genome sequences (WGS) where 386 WGS were from known nine coronavirus species.	WGS suggested: None
   The dataset was then aligned with MUSCLE [24].	MUSCLE suggested: (MUSCLE, RRID:SCR_011812)
   Entropy (H(x)) plot of nucleotide variations in SARS-CoV-2 genome was constructed using BioEdit [25].	BioEdit suggested: (BioEdit, RRID:SCR_007361)
   MEGA X (version 10.1.7) was used to construct the MSAs and the phylogenetic tree using pairwise alignment and neighbor-joining methods in ClustalW [26,27].	ClustalW suggested: (ClustalW, RRID:SCR_017277)
   The overall quality of models was assessed in RAMPAGE server [31] by generating Ramachandran plots (Supplementary Table 1).	RAMPAGE suggested: (RAMPAGE, RRID:SCR_017590)
   PyMol and BIOVIA Discovery Studio were used for structure visualization and superpose [32,33].	PyMol suggested: (PyMOL, RRID:SCR_000305)

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   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04321096	Active, not recruiting	The Impact of Camostat Mesilate on COVID-19 Infection

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 26, 22 and 23. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   Results from rtransparent:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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3. 

   Version published to 10.1101/2020.04.07.030924v1 on bioRxiv

   Apr 11, 2020