A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2

  1. Umar Faruq Chowdhury
  2. Mohammad Umer Sharif Shohan
  3. Kazi Injamamul Hoque
  4. Mirza Ashikul Beg
  5. Mohammad Kawsar Sharif Siam
  6. Mohammad Ali Moni

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Abstract

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  1. Version published to 10.1016/j.ygeno.2020.12.021
  2. ScreenIT

    SciScore for 10.1101/2020.04.10.036335: (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
    Multiple sequence alignment & phylogenetic tree construction: ClustalW [38] algorithm was employed to perform multiple sequence alignment.
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    Target recognition & siRNA designing: Target-specific siRNAs were designed with the help of siDirect web server [43].
    siDirect
    suggested: (siDirect, RRID:SCR_004853)
    Off target similarity search using BLAST: Blast search was performed against human genome and transcriptome using the standalone blast package [47] to identify the possible off target matches.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)

    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.
    • 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 10.1101/2020.04.10.036335v2 on bioRxiv
  4. Version published to 10.1101/2020.04.10.036335v3 on bioRxiv
  5. Version published to 10.1101/2020.04.10.036335v1 on bioRxiv