Genome Warehouse: A Public Repository Housing Genome-Scale Data

Chen, Meili; Ma, Yingke; Wu, Song; Zheng, Xinchang; Kang, Hongen; Sang, Jian; Xu, Xiwei; Hao, Lili; Li, Zhaohua; Gong, Zheng; Xiao, Jingfa; Zhang, Zhang; Zhao, Wenming; Bào, Yīmíng

doi:10.1016/j.gpb.2021.04.001

Cited by 140 publications

(80 citation statements)

References 25 publications

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“…Also, CompoDynamics is equipped with several useful tools for online analysis and visualization, thus enabling users to perform comparative analysis of sequence compositions and features across various species and gene groups. Future developments of CompoDynamics include periodical update (at least once a year) of high-quality genomes and CDSs from NCBI RefSeq, GENCODE, and Genome Warehouse ( 45 ) in NGDC ( 46 ). Moreover, untranslated genomic regions, such as the untranslated regions (UTRs), mRNA introns and noncoding RNAs, will be added to characterize composition dynamics in a larger scale.…”

Section: Discussion and Future Developmentsmentioning

confidence: 99%

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics

Jiang

Feng

et al. 2021

Nucleic Acids Research

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Sequence compositions of nucleic acids and proteins have significant impact on gene expression, RNA stability, translation efficiency, RNA/protein structure and molecular function, and are associated with genome evolution and adaptation across all kingdoms of life. Therefore, a devoted resource of sequence compositions and associated features is fundamentally crucial for a wide range of biological research. Here, we present CompoDynamics (https://ngdc.cncb.ac.cn/compodynamics/), a comprehensive database of sequence compositions of coding sequences (CDSs) and genomes for all kinds of species. Taking advantage of the exponential growth of RefSeq data, CompoDynamics presents a wealth of sequence compositions (nucleotide content, codon usage, amino acid usage) and derived features (coding potential, physicochemical property and phase separation) for 118 689 747 high-quality CDSs and 34 562 genomes across 24 995 species. Additionally, interactive analytical tools are provided to enable comparative analyses of sequence compositions and molecular features across different species and gene groups. Collectively, CompoDynamics bears the great potential to better understand the underlying roles of sequence composition dynamics across genes and genomes, providing a fundamental resource in support of a broad spectrum of biological studies.

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Section: Discussion and Future Developmentsmentioning

confidence: 99%

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics

Jiang

Feng

et al. 2021

Nucleic Acids Research

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“…The raw sequencing data and the whole genome sequences reported in this paper have been deposited in the Genome Sequence Archive (GSA) [41] and Genome Warehouse (GWH) [42] in the National Genomics Data Center [43] , Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA: CRA003122) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa/browse/CRA003122, and (GWH: GWHAOJE01000000–GWHAOOX01000000) at https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=PRJCA003179&page=1.…”

Section: Methodsmentioning

confidence: 99%

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Song

Kang

et al. 2021

Genomics, Proteomics &Amp; Bioinformatics

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COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected before June 2, 2020. We identified a total of 347 mutated positions, 31 of which were over-represented in Pakistan. Meanwhile, we found over 1000 intra-host single-nucleotide variants (iSNVs). Several of them occurred concurrently, indicating possible interactions among them or coevolution. Some of the high-frequency iSNVs in Pakistan were not observed in the global population, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab ) of this cluster. Furthermore, 28 putative international introductions were identified, several of which are consistent with the epidemiological investigations. In all, this study has inferred the possible pathways of introduction and transmissions of SARS-CoV-2 in Pakistan, which could aid ongoing and future viral surveillance and COVID-19 control.

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“…The Genome Warehouse (GWH; https://ngdc.cncb.ac.cn/gwh ) is a public repository of genome-scale data for a wide range of species ( 18 ). By September 2021, GWH has housed a total of 20 606 submitted genome assemblies covering 1,251 species (Figure 2D ), presenting a doubled increase in contrast to the previous release (9337 assemblies in 2020).…”

Section: Recent Updatesmentioning

confidence: 99%

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

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2021

Nucleic Acids Research

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The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

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Genome Warehouse: A Public Repository Housing Genome-Scale Data

Cited by 140 publications

References 25 publications

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

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