A CLAssification of Mobile genetic Elements
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A CLAssification of Mobile genetic Elements
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ACLAME
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
ACLAME - A Classification of Mobile genetic Elements
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
aclame
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
Names
More detailed information about this field from each metasource.
A CLAssification of Mobile genetic Elements
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ACLAME
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
ACLAME - A Classification of Mobile genetic Elements
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
aclame
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
Other names: ACLAME, ACLAME - A Classification of Mobile genetic Elements, aclame
Names
More detailed information about this field from each metasource.
A CLAssification of Mobile genetic Elements
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ACLAME
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
ACLAME - A Classification of Mobile genetic Elements
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
aclame
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
This source may no longer be available. No known URL could be resolved successfully.
ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.
Description
More detailed information about this field from each metasource.
ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
A classification of genetic mobile elements
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
This database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
Webpage:
http://aclame.ulb.ac.be/Webpage
More detailed information about this field from each metasource.
http://aclame.ulb.ac.be/
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
More detailed information about this field from each metasource.
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
More detailed information about this field from each metasource.
http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
ACLAME: a CLAssification of Mobile genetic Elements, update 2010
PMID: 19933762
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
ACLAME: a CLAssification of Mobile genetic Elements
PMID: 14681355
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
ACLAME: a CLAssification of Mobile genetic Elements, update 2010
PMID: 19933762
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
ACLAME: a CLAssification of Mobile genetic Elements
PMID: 14681355
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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ACLAME: a CLAssification of Mobile genetic Elements, update 2010
PubMed citations: 148.
148 articles citing: ACLAME: a CLAssification of Mobile genetic Elements, update 2010
Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota. PMID:35913596
Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control. PMID:35732277
Expressions of resistome is linked to the key functions and stability of active rumen microbiome. PMID:35659381
Preclinical Safety Assessment of Bacillus subtilis BS50 for Probiotic and Food Applications. PMID:35630480
More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. PMID:35493727
Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen. PMID:35336126
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. PMID:35323968
Evidence for the Rapid and Divergent Evolution of Mycoplasmas: Structural and Phylogenetic Analysis of Enolases. PMID:35145997
SGP-C: A Broad Host Range Temperate Bacteriophage; Against Salmonella gallinarum. PMID:35095790
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. PMID:34871418
Host life-history traits influence the distribution of prophages and the genes they carry. PMID:34839698
Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. PMID:34803947
A review of the resistome within the digestive tract of livestock. PMID:34763729
Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina. PMID:34728656
Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China. PMID:34650532
TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. PMID:34517763
PHROG: families of prokaryotic virus proteins clustered using remote homology. PMID:34377978
Antibiotic resistance: Time of synthesis in a post-genomic age. PMID:34141134
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. PMID:34018328
digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes. PMID:34016050
Expanding Diversity of Firmicutes Single-Strand Annealing Proteins: A Putative Role of Bacteriophage-Host Arms Race. PMID:33959107
Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. PMID:33919474
Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics. PMID:33916668
Viruses in fermented foods: are they good or bad? Two sides of the same coin. PMID:33875222
Examining horizontal gene transfer in microbial communities. PMID:33846600
Combined effects of composting and antibiotic administration on cattle manure-borne antibiotic resistance genes. PMID:33795006
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes. PMID:33580146
Acquisition of pcnB [poly(A) polymerase I] genes via horizontal transfer from the β, γ-Proteobacteria. PMID:33502308
Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages. PMID:33275597
Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation. PMID:33257813
Localized effect of treated wastewater effluent on the resistome of an urban watershed. PMID:33215210
Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways. PMID:33109761
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. PMID:33074335
Isolation and Characterization of Nitrate-Reducing Bacteria as Potential Probiotics for Oral and Systemic Health. PMID:33042063
Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe. PMID:32937127
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. PMID:32873785
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. PMID:32841606
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes. PMID:32841233
Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful? PMID:32695079
Experimental approaches to tracking mobile genetic elements in microbial communities. PMID:32672812
Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. PMID:32231141
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System. PMID:32140141
Longitudinal survey of microbiome associated with particulate matter in a megacity. PMID:32127018
Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution. PMID:31950028
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PMID:31830054
Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities. PMID:31641046
Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca). PMID:31635158
Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter dublinensis Genotyping Based on CRISPR Locus Diversity. PMID:31555228
Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes. PMID:31409850
Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations. PMID:31146680
Systematic evasion of the restriction-modification barrier in bacteria. PMID:31097593
Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes. PMID:31068435
Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes. PMID:30899254
Mining, analyzing, and integrating viral signals from metagenomic data. PMID:30890181
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. PMID:30808697
Characteristics of the tree shrew gut virome. PMID:30807598
Genome Analysis of Shigella flexneri Serotype 3b Strain SFL1520 Reveals Significant Horizontal Gene Acquisitions Including a Multidrug Resistance Cassette. PMID:30715343
Draft Genome Sequence of Lactobacillus kefiri SGL 13, a Potential Probiotic Strain Isolated from Kefir Grains. PMID:30533877
Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain. PMID:30497380
Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. PMID:30409177
Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy. PMID:30016225
Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant. PMID:29858829
MetaCompare: a computational pipeline for prioritizing environmental resistome risk. PMID:29718191
Design of a Broad-Range Bacteriophage Cocktail That Reduces Pseudomonas aeruginosa Biofilms and Treats Acute Infections in Two Animal Models. PMID:29555626
Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity. PMID:29523551
Draft Genome Sequence of Lactobacillus salivarius SGL 03, a Novel Potential Probiotic Strain. PMID:29217794
Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus. PMID:29058585
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. PMID:29028989
Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen. PMID:28979253
Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH. PMID:28961970
Review article: the human intestinal virome in health and disease. PMID:28869283
Pan-genome and phylogeny of Bacillus cereus sensu lato. PMID:28768476
Bacteriophage evolution differs by host, lifestyle and genome. PMID:28692019
The Threat of Antimicrobial Resistance on the Human Microbiome. PMID:28492988
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. PMID:28449715
Regulation of solvent tolerance in Pseudomonas putida S12 mediated by mobile elements. PMID:28401676
Mixed transmission modes and dynamic genome evolution in an obligate animal-bacterial symbiosis. PMID:28234348
Evolutionary and functional implications of hypervariable loci within the skin virome. PMID:28194314
Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. PMID:28106880
The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine? PMID:28090383
The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii. PMID:28057934
Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes. PMID:27917931
Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample. PMID:27565618
Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering. PMID:27444945
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". PMID:27303384
A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections. PMID:27301427
Transplanting a Microbial Organ: the Good, the Bad, and the Unknown. PMID:27143392
A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. PMID:27046334
Horizontal transfer of β-carbonic anhydrase genes from prokaryotes to protozoans, insects, and nematodes. PMID:26983858
Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PMID:26808278
H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PMID:26789284
Draft Genome Sequence of Actinobaculum massiliense Strain FC3. PMID:26769930
Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. PMID:26428854
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes. PMID:26200753
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. PMID:26200428
Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. PMID:26173980
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. PMID:26137199
Characterization of the Newly Isolated Lytic Bacteriophages KTN6 and KT28 and Their Efficacy against Pseudomonas aeruginosa Biofilm. PMID:25996839
Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon. PMID:25978546
Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations. PMID:25944863
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. PMID:25914678
A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604 (ATCC 27647). PMID:25628219
Automated classification of tailed bacteriophages according to their neck organization. PMID:25428721
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. PMID:25342549
Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics. PMID:25279954
Identification of the minimal replicon and the origin of replication of the crenarchaeal plasmid pRN1. PMID:25060695
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. PMID:24997787
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. PMID:24438450
Metabolic reprogramming by viruses in the sunlit and dark ocean. PMID:24200126
Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012. PMID:24067958
Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach. PMID:23760301
CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites. PMID:23671590
CRISPR regulation of intraspecies diversification by limiting IS transposition and intercellular recombination. PMID:23661565
Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. PMID:23651955
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. PMID:23628424
A mobile genetic element with unknown function found in distantly related viruses. PMID:23618040
Thermo-regulation of genes mediating motility and plant interactions in Pseudomonas syringae. PMID:23527276
The low incidence of diversity-generating retroelements in sequenced genomes. PMID:23481467
Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome. PMID:23386843
TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases. PMID:23251097
An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales. PMID:23234643
Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PMID:23226415
Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. PMID:23084289
Comparative sequence analysis of a multidrug-resistant plasmid from Aeromonas hydrophila. PMID:23070174
Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens. PMID:23035931
Going viral: next-generation sequencing applied to phage populations in the human gut. PMID:22864264
Stability of a Pseudomonas putida KT2440 bacteriophage-carried genomic island and its impact on rhizosphere fitness. PMID:22843519
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. PMID:22773627
Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content. PMID:22587570
Sequence Analysis of Inducible Prophage phIS3501 Integrated into the Haemolysin II Gene of Bacillus thuringiensis var israelensis ATCC35646. PMID:22567391
Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes. PMID:22502997
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Bacteriophages and their genomes. PMID:22034588
The influence of the accessory genome on bacterial pathogen evolution. PMID:22016845
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. PMID:22009673
Phamerator: a bioinformatic tool for comparative bacteriophage genomics. PMID:21991981
The human gut virome: inter-individual variation and dynamic response to diet. PMID:21880779
Genome-wide protein localization prediction strategies for gram negative bacteria. PMID:21810203
Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. PMID:21282711
Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. PMID:21097633
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. PMID:20929871
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. PMID:20435682
Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. PMID:20194117 -
ACLAME: a CLAssification of Mobile genetic Elements
PubMed citations: 88.
88 articles citing: ACLAME: a CLAssification of Mobile genetic Elements
More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. PMID:35493727
Review and Comparison of Antimicrobial Resistance Gene Databases. PMID:35326803
The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease. PMID:35092426
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. PMID:34517763
Acquisition of pcnB [poly(A) polymerase I] genes via horizontal transfer from the β, γ-Proteobacteria. PMID:33502308
Migratory birds-one major source of environmental antibiotic resistance around Qinghai Lake, China. PMID:32540654
Metagenomics as a Tool To Monitor Reclaimed-Water Quality. PMID:32503906
Dialister massiliensis sp. nov., a new bacterium isolated from the human gut. PMID:32194963
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. PMID:32071725
Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum. PMID:31011427
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. PMID:30808697
Characteristics of the tree shrew gut virome. PMID:30807598
Reconsidering plasmid maintenance factors for computational plasmid design. PMID:30619542
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem. PMID:30356154
Host-linked soil viral ecology along a permafrost thaw gradient. PMID:30013236
Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses. PMID:29969110
A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437. PMID:28831124
Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene. PMID:28495759
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PMID:28480138
Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses. PMID:28316597
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights. PMID:28095778
The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine? PMID:28090383
Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. PMID:28056800
Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes. PMID:27909433
Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes - Characterization of a Novel Phage Helper-Satellite System. PMID:27387973
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges. PMID:27375355
Graph mining for next generation sequencing: leveraging the assembly graph for biological insights. PMID:27154001
(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans. PMID:27151933
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. PMID:27025251
High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection. PMID:26882266
Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC). PMID:26555076
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. PMID:26489866
Direct sequencing of human gut virome fractions obtained by flow cytometry. PMID:26441889
Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. PMID:25954269
Targeted diversity generation by intraterrestrial archaea and archaeal viruses. PMID:25798780
Integrative workflows for metagenomic analysis. PMID:25478562
Comparative genomic analysis of Mycobacterium iranicum UM_TJL against representative mycobacterial species suggests its environmental origin. PMID:25417557
Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces. PMID:25417012
CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography. PMID:25344663
Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas--Erysipelothrix rhusiopathiae SY1027. PMID:24993343
Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151. PMID:24278159
Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences. PMID:24036533
Complete genome analysis of a Haemophilus parasuis serovar 12 strain from China. PMID:24023711
The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria. PMID:23678183
Short and long-term genome stability analysis of prokaryotic genomes. PMID:23651581
A mobile genetic element with unknown function found in distantly related viruses. PMID:23618040
VIROME: a standard operating procedure for analysis of viral metagenome sequences. PMID:23407591
Comparative sequence analysis of a multidrug-resistant plasmid from Aeromonas hydrophila. PMID:23070174
Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. PMID:23038177
Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution. PMID:22965120
Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. PMID:22923589
Evidence of in vivo prophage induction during Clostridium difficile infection. PMID:22923402
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. PMID:22584627
Insights into the bovine rumen plasmidome. PMID:22431592
Major families of multiresistant plasmids from geographically and epidemiologically diverse staphylococci. PMID:22384369
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. PMID:22258098
Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. PMID:22126996
Mycobacteriophage genome database. PMID:21904429
TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. PMID:21886867
Prophage-stimulated toxin production in Clostridium difficile NAP1/027 lysogens. PMID:21441508
Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts. PMID:21317336
Metagenomic analysis of the viral communities in fermented foods. PMID:21183634
Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss. PMID:21126366
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. PMID:21036865
Mobility of plasmids. PMID:20805406
Unraveling the viral tapestry (from inside the capsid out). PMID:20555364
Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. PMID:20333191
Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. PMID:20194117
Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. PMID:20067338
Genome organization and characterization of the virulent lactococcal phage 1358 and its similarities to Listeria phages. PMID:20061452
Genomic characterization of the Yersinia genus. PMID:20047673
ACLAME: a CLAssification of Mobile genetic Elements, update 2010. PMID:19933762
ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. PMID:19906702
The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'. PMID:19840100
Integrative and sequence characteristics of a novel genetic element, ICE6013, in Staphylococcus aureus. PMID:19648240
What we can learn about Escherichia coli through application of Gene Ontology. PMID:19576778
Conjugative plasmids: vessels of the communal gene pool. PMID:19571247
Shared catalysis in virus entry and bacterial cell wall depolymerization. PMID:19361422
High-resolution mapping of plasmid transcriptomes in different host bacteria. PMID:19134166
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. PMID:18803844
Microbial ecology of four coral atolls in the Northern Line Islands. PMID:18301735
Systematic identification of stem-loop containing sequence families in bacterial genomes. PMID:18201379
Bottleneck genes and community structure in the cell cycle network of S. pombe. PMID:17542643
Towards pathogenomics: a web-based resource for pathogenicity islands. PMID:17090594
ISfinder: the reference centre for bacterial insertion sequences. PMID:16381877
Tags:
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
coding and non-coding dna
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
mobile genetic elements
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
genetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
protein interaction experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:14.949155
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: ACLAME; A CLAssification of Mobile genetic Elements; DOI: https://doi.org/10.25504/FAIRsharing.5tfcy8; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
coding and non-coding dna
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
mobile genetic elements
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
genetics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
protein interaction experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:14.949155
gene genome nucleic acid sequence coding and non-coding dna mobile genetic elements gene and protein families model organisms genetics protein interaction experiment
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