Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2

  1. Intikhab Alam
  2. Allan A. Kamau
  3. Maxat Kulmanov
  4. Łukasz Jaremko
  5. Stefan T. Arold
  6. Arnab Pain
  7. Takashi Gojobori
  8. Carlos M. Duarte

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Abstract

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  1. Version published to 10.3389/fcimb.2020.00405
  2. ScreenIT

    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
    SentencesResources
    AAMG uses sequence-based BLAST to UniProtKB (www.uniprot.org),
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    UniProtKB
    suggested: (UniProtKB, RRID:SCR_004426)
    KEGG (www.kegg.jp) and also Protein Family (PFam) domain detection using InterPro (www.ebi.ac.uk/interpro).
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    PFam
    suggested: (Pfam, RRID:SCR_004726)
    InterPro
    suggested: (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.
    QuickGO
    suggested: (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.
    ProtParam
    suggested: (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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.02.17.952895v2 on bioRxiv
  4. Version published to 10.1101/2020.02.17.952895v1 on bioRxiv