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database Commons:A Catalog of Worldwide biological databases

Genomics, Proteomics & Bioinformatics 2023年第5期21卷 1054-1058页

作者： Lina Ma Dong Zou Lin Liu Huma Shireen Amir AAbbasi Alex Bateman Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China National Center for Bioinformatics Programme of Comparative and Evolutionary GenomicsFaculty of Biological SciencesQuaid-i-Azam UniversityIslamabad 45320Pakistan European Molecular Biology Laboratory European Bioinformatics Institute(EMBL-EBI)HinxtonCambridge CB101SDUnited Kingdom

biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research *** the rapid data production,biological databases continue to increase in size and *** build a catalog of worldwide biological databases,we curate a total of 5825 biological databases from 8931 publications,which are geographically distributed in 72 countries/regions and developed by 1975 institutions(as of September 20,2022).We further devise a z-index,a novel index to characterize the scientific impact of a database,and rank all these biological databases as well as their hosting institutions and countries in terms of citation and ***,we present a series of statistics and trends of worldwide biological databases,yielding a global perspective to better understand their status and impact for life and health *** up-to-date catalog of worldwide biological databases,as well as their curated meta-information and derived statistics,is publicly available at database Commons(https://***/databasecommons/).

关键词： biological database Catalog database Commons Citation z-index

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ICEr;a web-based tool for rapid identification of integrative and conjugative elements in bacterial genomes

ICEr;a web-based tool for rapid identification of integrativ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Dexi Bi Hong-Yu Ou State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology Shanghai Jiaotong University

Background:Integrative and conjugative elements(ICEs) are bacterial selftransmissible elements that encode a full complement of machinery for conjugation as well as excision from the chromosome and onward conjugative *** can promote their own mobilization and potentially that of other ’hitch-hiking’ mobile genetic elements,and thus contribute to horizontal transfer of virulence determinants,antibiotic-resistance genes and other bacterial *** sequenced genome databases expand exponentially,ICEs have been identified in increasing *** we have developed a web-based tool ICEr for rapid identification of ICEs in bacterial genomes,supported by the back-end database ICEberg. Methods:The web-based database ICEberg currently contained details of 428 ICEs found in representatives of 124 bacteria! species,and a collection of over four hundred directly related references[Bi,et al.,Nucleic Acids Research,2012].Although ICEs vary in sequence and genetic organization,sequence comparison and phylogenetic analysis showed showed that many share related integrase,maintenance and/or transfer *** thus classified 344 ICE entries as 28 specific families firstly based on integrase similarity and secondarily core structure synteny. Recently an online tool ICEr have been delevoped for identification of ICEs in bacterial genome *** integrated the Vmatch program to detect the ICE-flanking direct repeats and HMMER3 for the homology searches of the specific ICE repertoire,including integrase,relaxase and/or type IV secretion system,which had been archived within ICEberg. Users can upload their bacterial nucleotide sequence with or without *** parallel computing cluster architecture,typically ICEr idenify the putive ICEs ’on the fly’ in a matter of 1～5 *** example,it takes ca.1 minute for the annotated 5.3 Mb Klebsiella pneumoniae clinical isolate *** novel ICEs were found within the HS11286 chromosome,an 62-kb element e

关键词： integrative and conjugative elements conjugative transposon biological database in silico predicton tool Klebsiella pneumoniae

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