The 2021 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection

Rigden, Daniel J.; Fernández, Xosé M.

doi:10.1093/nar/gkaa1216

Cited by 48 publications

(27 citation statements)

References 87 publications

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“… Rigden and Fernández 2021 2021 Covid+other Table 89 Nucleic Acids Res. [22] Rigden and Fernández 2020 2020 Nucleic acid Table 70 Nucleic Acids Res. [18] Xu 2012 2012 Protein Table 121 Curr.…”

Section: Resultsmentioning

confidence: 99%

An innovative user-friendly platform for Covid-19 pandemic databases and resources

Ullah¹,

Ullah²,

Rahman³

et al. 2021

Computer Methods and Programs in Biomedicine Update

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Background COVID-19 is a global outbreak of a disease from a new virus, occurred in Wuhan China in December 2019. Several databases have been published on this pandemic, but the research community still needs an easy way to get comprehensive information on COVID-19. Objectives COVID-19 pandemic database (CO-19 PDB) aims to provide wonderful insights for COVID-19 researchers with the well-gathered of all the COVID-19 data to one platform, which is a global challenge for the research community these days. Methods We gathered 59 updated databases since December-2019 until May 2021 and divided them into six categories: digital image database, genomic database, literature database, visualization tools database, chemical structure database, and social science database. These categories focus on taking number of functions from the images, information from gene sequences, updates from relevant papers, essays, reports, articles, and books, the data or information in the form of maps, graphs, and charts, information of bonds between atoms, and updates about events of the physical and social environment, respectively. Results Users can search the information of interest in two ways including typing the name of the database in the search bar or by clicking the right category directly. Computer languages such as CSS, PHP, HTML, Java, etc. are utilized to construct CO-19 PDB. Conclusion This article attempts to compile up-to-date appropriate COVID-19 datasets and resources that have not been compiled and given in such an accessible and user-friendly manner. As a result, the CO-19 PDB offers extensive open data sharing for both worldwide research communities and local people. Further, we have planned future development of new features, that will be awesome for future study.

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Section: Resultsmentioning

confidence: 99%

An innovative user-friendly platform for Covid-19 pandemic databases and resources

Ullah¹,

Ullah²,

Rahman³

et al. 2021

Computer Methods and Programs in Biomedicine Update

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“…UniProt [ 22 ] was used to access the protein sequences in this analysis ( Table 1 ). UniProt is an opensource database maintained by the UniProt consortium.…”

Section: Methodsmentioning

confidence: 99%

“…Protein sequences were downloaded from UniProt and then aligned using MultiAlin [ 22 , 26 ]. Pediocin, Divercin, Microcin and Enterocin were uploaded to the server, default parameters of 90% high consensus and 50% low consensus were used.…”

Section: Methodsmentioning

confidence: 99%

Exploring the cytotoxic mechanisms of Pediocin PA-1 towards HeLa and HT29 cells by comparison to known bacteriocins: Microcin E492, enterocin heterodimer and Divercin V41

Buss

Wilson

2021

PLoS ONE

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The purpose of this study was to explore potential mechanisms of cytotoxicity towards HeLa and HT29 cells displayed by Pediocin PA-1. We did this by carrying out sequence alignments and 3D modelling of related bacteriocins which have been studied in greater detail: Microcin E492, Enterocin AB heterodimer and Divercin V41. Microcin E492 interacts with Toll-Like Receptor 4 in order to activate an apoptosis reaction, sequence alignment showed a high homology between Pediocin PA-1 and Microcin E492 whereas 3D modelling showed Pediocin PA-1 interacting with TLR-4 in a way reminiscent of Microcin E492. Furthermore, Pediocin PA-1 had the highest homology with the Enterocin heterodimer, particularly chain A; Enterocin has also shown to cause an apoptotic response in cancer cells. Based on this we are led to strongly believe Pediocin PA-1 interacts with TLRs in order to cause cell death. If this is the case, it would explain the difference in cytotoxicity towards HeLa over HT29 cells, due to difference in expression of particular TLRs. Overall, we believe Pediocin PA-1 exhibits a dual effect which is dose dependant, like that of Microcin. Unfortunately, due to the COVID-19 pandemic, we were unable to carry out experiments in the lab, and the unavailability of important data meant we were unable to provide and validate out solid conclusions, but rather suggestions. However, bioinformatic analysis is still able to provide information regarding structure and sequence analysis to draw plausible and evidence based conclusions. We have been able to highlight interesting findings and how these could be translated into future research and therapeutics in order to improve the quality of treatment and life of cancer patients.

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“…oxfor djour nals. org/ our_ journ als/ nar/ datab ase/ cap/), with new compendiums appearing yearly to meet evolving biological interests (Rigden and Fernández 2021). Many of the databases that underpin metagenomic analysis are not specific for the purpose.…”

Section: Reference Databases For Taxonomic Classificationmentioning

confidence: 99%

Metagenomics: a path to understanding the gut microbiome

Yen

Johnson

2021

Mamm Genome

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The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.

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The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

Cited by 48 publications

References 87 publications

An innovative user-friendly platform for Covid-19 pandemic databases and resources

An innovative user-friendly platform for Covid-19 pandemic databases and resources

Exploring the cytotoxic mechanisms of Pediocin PA-1 towards HeLa and HT29 cells by comparison to known bacteriocins: Microcin E492, enterocin heterodimer and Divercin V41

Metagenomics: a path to understanding the gut microbiome

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