A database resource for Genome-wide dynamics analysis of Coronaviruses on a historical and global scale
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Abstract
The recent outbreak of a new zoonotic origin Coronavirus has ring the bell for the potential spread of epidemic Coronavirus crossing the species. With the urgent needs to assist the control of the Coronavirus spread and to provide valuable scientific information, we developed a coronavirus database (CoVdb), an online genomics and proteomics analysis platform. Based on public available coronavirus genomic information, the database annotates the genome of every strain and identifies 780 possible ORFs of all strains available in Genebank. In addition, the comprehensive evaluation of all the published genomes of Coronavirus strains, including population genetics analysis, functional analysis and structural analysis on a historical and global scale were presented in the CoVdb. In the database, the researcher can easily obtain the basic information of a Coronavirus gene with the distribution of the gene among strains, conserved or high mutation regions, possible subcellular location and topology of the gene. Moreover, sliding windows for population genetics analysis results is provided, thereby facilitating genetics and evolutional analysis at the genomic level. CoVdb can be accessed freely at http://covdb.popgenetics.net .
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SciScore for 10.1101/2020.02.05.920009: (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 Using the accession number of matched UniProt proteins, we retrieved detailed proteomics information from UniProt. UniProtsuggested: (UniProtKB, RRID:SCR_004426)The results are used to built a phylogenetic tree by FastTree 2.134. FastTreesuggested: (FastTree, RRID:SCR_015501)CoVdb also incorporates MSAViewer42 to display multiple alignments and phylotree.js43 to show the phylogenetic trees. CoVdbsuggested: 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 Limitation…SciScore for 10.1101/2020.02.05.920009: (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 Using the accession number of matched UniProt proteins, we retrieved detailed proteomics information from UniProt. UniProtsuggested: (UniProtKB, RRID:SCR_004426)The results are used to built a phylogenetic tree by FastTree 2.134. FastTreesuggested: (FastTree, RRID:SCR_015501)CoVdb also incorporates MSAViewer42 to display multiple alignments and phylotree.js43 to show the phylogenetic trees. CoVdbsuggested: 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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- 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.
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