In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
SciScore for 10.1101/2020.04.09.031252: (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 All the results were merged into a single Microsoft Excel file where statistical analysis was then made. Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Features tables of 109 Nidovirales genomes were downloaded from the NCBI database and grouped by their names as stated in the feature table file. NCBIsuggested: (NCBI, RRID:SCR_006472)Complete analyses of IRs occurrence in Nidovirales are provided in Supplementary Material 4. 2.5 RNA Fold Predictions: In order to be able to display higher structures of the coronavirus genome, we used Galaxy’s free-online webserver (Afgan et al., … SciScore for 10.1101/2020.04.09.031252: (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 All the results were merged into a single Microsoft Excel file where statistical analysis was then made. Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Features tables of 109 Nidovirales genomes were downloaded from the NCBI database and grouped by their names as stated in the feature table file. NCBIsuggested: (NCBI, RRID:SCR_006472)Complete analyses of IRs occurrence in Nidovirales are provided in Supplementary Material 4. 2.5 RNA Fold Predictions: In order to be able to display higher structures of the coronavirus genome, we used Galaxy’s free-online webserver (Afgan et al., 2018) and its RNA fold tool (Lorenz et al., 2011). Galaxy’ssuggested: (BioBlend Library, RRID:SCR_014557)2.6 Multiple Alignment of SUD Domains (M Regions) in Nsp3 of Pathogenic Species: Multiple protein alignment was done using MUSCLE (Edgar, 2004) under default parameters (UGENE [Okonechnikov et al., 2012] workflow was used). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)The output was further filtered in Excel to keep only those hits below p-value = 1.10−6. Excelsuggested: NoneSupplementary Material 1: Summary of analyzed Nidovirales genomes (full names, phylogenetic groups, exact NCBI accession, and further information) Supplementary Material 2: Complete analyses of PQS occurrence in Nidovirales Supplementary Material 3: Categorization of IRs according to their overlap with a feature or feature neighborhood Supplementary Material 4: Complete analyses of IRs occurrence in Nidovirales Supplementary Material 5: RNA fold prediction for SARS-CoV2 RNA and random RNA of the same length and GC content Supplementary Material 6: Complete RBPmap results – Prediction of human RNA-binding protein sites in SARS-CoV-2 RNA Supplementary Material 7: Prediction of RGG-rich NIQI motifs in proteins identified by RBPmap RBPmapsuggested: NoneResults 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.
-
