Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism
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SciScore for 10.1101/2020.06.07.138800: (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 Identification of Nucleotide Variations in Bangladeshi Strain: We performed multiple sequence alignment using Clustal Omega [15, 16], and the sequence of the strain China [EPI_ISL_402124] was used as a reference genome. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Prediction of Viral Genome and Identification of Selected Genes: FGENESV of SoftBerry (http://linux1.softberry.com/berry.phtml), which is a Trained Pattern/Markov chain-based viral gene prediction tools, was adopted for the prediction of the genes as well as the proteins from the viral genomes. SoftBerrysuggested: …SciScore for 10.1101/2020.06.07.138800: (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 Identification of Nucleotide Variations in Bangladeshi Strain: We performed multiple sequence alignment using Clustal Omega [15, 16], and the sequence of the strain China [EPI_ISL_402124] was used as a reference genome. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Prediction of Viral Genome and Identification of Selected Genes: FGENESV of SoftBerry (http://linux1.softberry.com/berry.phtml), which is a Trained Pattern/Markov chain-based viral gene prediction tools, was adopted for the prediction of the genes as well as the proteins from the viral genomes. SoftBerrysuggested: (SoftBerry, RRID:SCR_000902)Homology Modeling of Spike Proteins and Validation: The BLASTp program at the NCBI interface (link) was used to find the most suitable template for homology modeling. BLASTpsuggested: (BLASTP, RRID:SCR_001010)First, the crystal structure of human ACE2 (PDB ID 6D0G) was obtained from Protein Data Bank, and PyMOL was used to clean the structure to remove all the complex molecules and water [24, 25]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)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).
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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