SARS-CoV-2 3CLpro whole human proteome cleavage prediction and enrichment/depletion analysis
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
SciScore for 10.1101/2020.08.24.265645: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources 70] Searching for “orf1ab,” “pp1ab,” and “1ab” within the family Coronaviridae returned 388 different, complete polyproteins with 762 different cleavages manually discovered using the Clustal Omega multiple sequence alignment server.[71–73] All 4,268 balanced positive cleavages were used for subsequent classifier training in addition to all other uncleaved coronavirus sequence windows centered at glutamines (17,493) and histidines (11,421), totaling 33,182 samples. Clustal Omegasu…SciScore for 10.1101/2020.08.24.265645: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources 70] Searching for “orf1ab,” “pp1ab,” and “1ab” within the family Coronaviridae returned 388 different, complete polyproteins with 762 different cleavages manually discovered using the Clustal Omega multiple sequence alignment server.[71–73] All 4,268 balanced positive cleavages were used for subsequent classifier training in addition to all other uncleaved coronavirus sequence windows centered at glutamines (17,493) and histidines (11,421), totaling 33,182 samples. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Enrichment Analysis: Protein annotation, classification, and enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) 6.8.[75, 76] My training data, prediction methods, and results can be found on GitHub (https://github.com/Luke8472NN/NetProtease). DAVIDsuggested: (DAVID, RRID:SCR_001881)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.
-
-