Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2
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SciScore for 10.1101/2020.02.17.952895: (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 AAMG uses sequence-based BLAST to UniProtKB (www.uniprot.org), BLASTsuggested: (BLASTX, RRID:SCR_001653)UniProtKBsuggested: (UniProtKB, RRID:SCR_004426)KEGG (www.kegg.jp) and also Protein Family (PFam) domain detection using InterPro (www.ebi.ac.uk/interpro). KEGGsuggested: (KEGG, RRID:SCR_012773)PFamsuggested: (Pfam, RRID:SCR_004726)InterProsuggested: (InterPro, RRID:SCR_006695)Predicted Gene Ontology (GO) terms with a confidence score from DeepGOPlus were visualized using QuickGO (https://www.ebi.ac.uk/QuickGO/) for SARS-CoV-2 specific gene clusters. QuickGOsuggested: (QuickGO, RRID:SCR_004…SciScore for 10.1101/2020.02.17.952895: (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 AAMG uses sequence-based BLAST to UniProtKB (www.uniprot.org), BLASTsuggested: (BLASTX, RRID:SCR_001653)UniProtKBsuggested: (UniProtKB, RRID:SCR_004426)KEGG (www.kegg.jp) and also Protein Family (PFam) domain detection using InterPro (www.ebi.ac.uk/interpro). KEGGsuggested: (KEGG, RRID:SCR_012773)PFamsuggested: (Pfam, RRID:SCR_004726)InterProsuggested: (InterPro, RRID:SCR_006695)Predicted Gene Ontology (GO) terms with a confidence score from DeepGOPlus were visualized using QuickGO (https://www.ebi.ac.uk/QuickGO/) for SARS-CoV-2 specific gene clusters. QuickGOsuggested: (QuickGO, RRID:SCR_004608)s Structure based prediction of function: ProtParam (https://web.expasy.org/cgi-bin/protparam/protparam) was used for calculating protein features. ProtParamsuggested: (ProtParam Tool, RRID:SCR_018087)Phobius (http://phobius.sbc.su.se/) and SignalP-5.0 were used for prediction of transmembrane regions and signal peptides 28. http://phobius.sbc.su.se/suggested: (Phobius, RRID:SCR_015643)Results from OddPub: Thank you for sharing your code.
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: Please consider improving the rainbow (“jet”) colormap(s) used on page 14. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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