Genome Properties
Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. This is a reimplementation at EMBL-EBI of a resource previously hosted at JCVI.
Description
More detailed information about this field from each metasource.
Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. This is a reimplementation at EMBL-EBI of a resource previously hosted at JCVI.
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Webpage:
https://www.ebi.ac.uk/interpro/genomepropertiesWebpage
More detailed information about this field from each metasource.
https://www.ebi.ac.uk/interpro/genomeproperties
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Licence:
Name: EMBL-EBI Terms of UseLicence name
More detailed information about this field from each metasource.
EMBL-EBI Terms of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Licence URL
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/about/terms-of-use
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
TIGRFAMs and Genome Properties in 2013
PMID: 23197656
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
PMID: 17151080
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
PMID: 15347579
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes
PMID: 30364992
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications
More detailed information about this field from each metasource.
TIGRFAMs and Genome Properties in 2013
PMID: 23197656
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
PMID: 17151080
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
PMID: 15347579
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes
PMID: 30364992
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
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TIGRFAMs and Genome Properties in 2013
PubMed citations: 247.
247 articles citing: TIGRFAMs and Genome Properties in 2013
Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PMID:35901096
ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PMID:35774624
Orrella daihaiensis sp. nov., a bacterium isolated from Daihai Lake in Inner Mongolia. PMID:35751751
Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales. PMID:35735993
Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin. PMID:35717543
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. PMID:35580059
Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. PMID:35495730
The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design. PMID:35441092
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PMID:35417463
Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples. PMID:35404108
Identification of a poly-cyclopropylglycine-containing peptide via bioinformatic mapping of radical S-adenosylmethionine enzymes. PMID:35367210
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L. PMID:35328546
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Piffle. PMID:35319268
Heterologous Expression and Biochemical Analysis Reveal a Schizokinen-Based Siderophore Pathway in Leptolyngbya (Cyanobacteria). PMID:35285240
Deciphering the Potential Coding of Human Cytomegalovirus: New Predicted Transmembrane Proteome. PMID:35269907
Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. PMID:35258341
DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp. PMID:35089065
Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus. PMID:35022698
A quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infection. PMID:34992142
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. PMID:34991452
The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools. PMID:34828362
Type IX Secretion System Effectors and Virulence of the Model Flavobacterium columnare Strain MS-FC-4. PMID:34818105
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. PMID:34791313
A computational screen for alternative genetic codes in over 250,000 genomes. PMID:34751130
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes. PMID:34627149
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer. PMID:34442840
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. PMID:34341414
IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context. PMID:34276598
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. PMID:34241589
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. PMID:34227932
Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. PMID:34220764
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
DOE JGI Metagenome Workflow. PMID:34006627
DoChaP: the domain change presenter. PMID:33988713
Comparative genomics and analysis of the mechanism of PQQ overproduction in Methylobacterium. PMID:33983497
antiSMASH 6.0: improving cluster detection and comparison capabilities. PMID:33978755
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. PMID:33941076
A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. PMID:33931420
Best practices on the differential expression analysis of multi-species RNA-seq. PMID:33926528
A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. PMID:33902712
Draft genome of a biparental beetle species, Lethrus apterus. PMID:33902445
Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. PMID:33888068
A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes. PMID:33815444
Putative LysM Effectors Contribute to Fungal Lifestyle. PMID:33808705
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications. PMID:33585410
Four families of folate-independent methionine synthases. PMID:33534785
The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensis. PMID:33505439
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
CheckV assesses the quality and completeness of metagenome-assembled viral genomes. PMID:33349699
Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. PMID:33283865
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. PMID:33270901
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. PMID:33167031
The InterPro protein families and domains database: 20 years on. PMID:33156333
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. PMID:33013723
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
New developments in RiPP discovery, enzymology and engineering. PMID:32935693
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery. PMID:32873609
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. PMID:32859984
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection. PMID:32722163
Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae. PMID:32605988
Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species. PMID:32589566
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. PMID:32576248
The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium psychrophilum. PMID:32532872
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. PMID:32427317
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Site-Specific Conditions Change the Response of Bacterial Producers of Soil Structure-Stabilizing Agents Such as Exopolysaccharides and Lipopolysaccharides to Tillage Intensity. PMID:32318044
Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing. PMID:32174973
First draft genome for the sand-hopper Trinorchestia longiramus. PMID:32152293
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Clades of huge phages from across Earth's ecosystems. PMID:32051592
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. PMID:31988473
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics. PMID:31957879
Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation. PMID:31920012
Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. PMID:31879772
NCBI's Conserved Domain Database and Tools for Protein Domain Analysis. PMID:31851420
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. PMID:31842745
CDD/SPARCLE: the conserved domain database in 2020. PMID:31777944
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
Local Adaptation of Bacterial Symbionts within a Geographic Mosaic of Antibiotic Coevolution. PMID:31676475
Clade II Candida auris possess genomic structural variations related to an ancestral strain. PMID:31596885
Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides. PMID:31372685
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. PMID:31267135
The Carboxy-Terminal Region of Flavobacterium johnsoniae SprB Facilitates Its Secretion by the Type IX Secretion System and Propulsion by the Gliding Motility Machinery. PMID:31262839
Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides. PMID:31059252
Nucleotide Second Messenger-Based Signaling in Extreme Acidophiles of the Acidithiobacillus Species Complex: Partition Between the Core and Variable Gene Complements. PMID:30899248
New insights from uncultivated genomes of the global human gut microbiome. PMID:30867587
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. PMID:30746495
A new genomic blueprint of the human gut microbiota. PMID:30745586
The neuroactive potential of the human gut microbiota in quality of life and depression. PMID:30718848
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. PMID:30692531
Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals. PMID:30687279
Investigating Lactococcus lactis MG1363 Response to Phage p2 Infection at the Proteome Level. PMID:30679258
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production. PMID:30572955
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. PMID:30533809
Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry. PMID:30504213
Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. PMID:30429574
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing. PMID:30355765
The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. PMID:30340631
Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus. PMID:30305867
Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. PMID:30291328
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. PMID:30289528
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. PMID:30123662
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13. PMID:29954895
How accurate is automated gap filling of metabolic models? PMID:29914471
HMMER web server: 2018 update. PMID:29905871
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
Identification of a unique Radical SAM methyltransferase required for the sp3-C-methylation of an arginine residue of methyl-coenzyme M reductase. PMID:29743535
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
Flexible metagenome analysis using the MGX framework. PMID:29690922
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. PMID:29662147
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Two-Component Flavin-Dependent Riboflavin Monooxygenase Degrades Riboflavin in Devosia riboflavina. PMID:29610214
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. PMID:29492869
Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics. PMID:29483940
Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium. PMID:29472337
Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria. PMID:29359196
Methanobactins: Maintaining copper homeostasis in methanotrophs and beyond. PMID:29348173
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PMID:29324779
Metals and Methanotrophy. PMID:29305514
Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone. PMID:29259587
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. PMID:29244774
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
RefSeq: an update on prokaryotic genome annotation and curation. PMID:29112715
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. PMID:29112695
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. PMID:29106469
Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective. PMID:28973392
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
PATRIC as a unique resource for studying antimicrobial resistance. PMID:28968762
Microbial genome analysis: the COG approach. PMID:28968633
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. PMID:28873963
Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production. PMID:28865010
Association of coral algal symbionts with a diverse viral community responsive to heat shock. PMID:28818037
A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate. PMID:28775791
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Helicobacter pylori gene silencing in vivo demonstrates urease is essential for chronic infection. PMID:28644872
Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces. PMID:28588130
Validating regulatory predictions from diverse bacteria with mutant fitness data. PMID:28542589
InlL from Listeria monocytogenes Is Involved in Biofilm Formation and Adhesion to Mucin. PMID:28473809
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. PMID:28408760
Diverse C-Terminal Sequences Involved in Flavobacterium johnsoniae Protein Secretion. PMID:28396348
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
A comprehensive software suite for protein family construction and functional site prediction. PMID:28182651
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. PMID:28168014
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. PMID:28116042
Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium. PMID:28082484
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. PMID:28049838
Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium. PMID:27979952
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. PMID:27899676
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. PMID:27899674
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
Accelerating Information Retrieval from Profile Hidden Markov Model Databases. PMID:27875548
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. PMID:27802571
IMG/M: integrated genome and metagenome comparative data analysis system. PMID:27738135
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions. PMID:27552220
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9. PMID:27536339
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. PMID:27489856
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well. PMID:27375557
Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellín, Colombia. PMID:27313305
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. PMID:27065959
Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1. PMID:27056228
Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen. PMID:27056226
The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins. PMID:27010565
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
Identification of protein secretion systems in bacterial genomes. PMID:26979785
Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. PMID:26939581
Towards the bridging of molecular genetics data across Xenopus species. PMID:26925848
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. PMID:26903996
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PMID:26890609
Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite. PMID:26858705
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. PMID:26768901
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia. PMID:26566421
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. PMID:26541816
Draft-genome sequence of Shewanella algae strain C6G3. PMID:26380631
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Pan-Tetris: an interactive visualisation for Pan-genomes. PMID:26328606
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. PMID:26257709
Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. PMID:26203326
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Molecular mechanisms underlying the close association between soil Burkholderia and fungi. PMID:25989372
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
HMMER web server: 2015 update. PMID:25943547
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. PMID:25780506
Improving the consistency of domain annotation within the Conserved Domain Database. PMID:25767294
Structure and function of the bacterial root microbiota in wild and domesticated barley. PMID:25732064
A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). PMID:25673765
Using comparative genomics to drive new discoveries in microbiology. PMID:25617609
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. PMID:25520706
An ancient autoproteolytic domain found in GAIN, ZU5 and Nucleoporin98. PMID:25451782
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
CDD: NCBI's conserved domain database. PMID:25414356
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. PMID:25398900
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PMID:25330359
MetaProx: the database of metagenomic proximons. PMID:25288655
Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. PMID:25168586
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. PMID:25161238
Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. PMID:25072413
SFannotation: A Simple and Fast Protein Function Annotation System. PMID:25031571
Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea. PMID:24999826
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium. PMID:24604643
Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PMID:24475038
InterProScan 5: genome-scale protein function classification. PMID:24451626
SeqDepot: streamlined database of biological sequences and precomputed features. PMID:24234005
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
Interaction between the genomes of Lactococcus lactis and phages of the P335 species. PMID:24009606
The Complete Genome Sequence of Methanobrevibacter sp. AbM4. PMID:23991254
Metagenomic guilt by association: an operonic perspective. PMID:23940763
Detoxification of mercury by methanobactin from Methylosinus trichosporium OB3b. PMID:23872554
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. PMID:23863837
Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. PMID:23535141
Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. PMID:23477283
Genome mining for methanobactins. PMID:23442874 -
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
PubMed citations: 154.
154 articles citing: TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Phylogeny-Informed Synthetic Biology Reveals Unprecedented Structural Novelty in Type V Glycopeptide Antibiotics. PMID:35647273
Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. PMID:35468809
A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. PMID:35328559
Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. PMID:35173296
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice. PMID:34851167
Hydrogen Peroxide Affects Growth of S. aureus Through Downregulation of Genes Involved in Pyrimidine Biosynthesis. PMID:34557184
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. PMID:34493810
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. PMID:34408730
Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance. PMID:34163450
PanACoTA: a modular tool for massive microbial comparative genomics. PMID:33575648
Discovery of multi-operon colinear syntenic blocks in microbial genomes. PMID:32657415
Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. PMID:32655516
Gut metagenomic and short chain fatty acids signature in hypertension: a cross-sectional study. PMID:32296109
Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment. PMID:32269557
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Tools for Analysis of the Microbiome. PMID:32002757
Investigating the Multi-Target Pharmacological Mechanism of Hedyotis diffusa Willd Acting on Prostate Cancer: A Network Pharmacology Approach. PMID:31600936
Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota. PMID:31447484
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. PMID:31366912
In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. PMID:31316134
Trait-based analysis of the human skin microbiome. PMID:31277701
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. PMID:30651609
Metabolic adaptation in the human gut microbiota during pregnancy and the first year of life. PMID:30415891
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host. PMID:30231855
Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. PMID:30134835
Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation. PMID:30109428
Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake. PMID:30108167
Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities. PMID:30072968
Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs. PMID:29420776
Insights into origin and evolution of α-proteobacterial gene transfer agents. PMID:29250433
The genome draft of coconut (Cocos nucifera). PMID:29048487
Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron. PMID:28951891
Protein Bioinformatics Databases and Resources. PMID:28150231
The landscape of microbial phenotypic traits and associated genes. PMID:27915291
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine. PMID:27507967
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. PMID:27458440
The Ensembl gene annotation system. PMID:27337980
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. PMID:27118214
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). PMID:26512311
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. PMID:26097471
Label-free Quantitative Proteomics Reveals a Role for the Mycobacterium tuberculosis SecA2 Pathway in Exporting Solute Binding Proteins and Mce Transporters to the Cell Wall. PMID:25813378
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. PMID:25745418
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
Insect gut microbiome - An unexploited reserve for biotechnological application. PMID:25183073
Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. PMID:24885207
The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PMID:24516394
New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. PMID:24449752
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. PMID:24341328
IMG 4 version of the integrated microbial genomes comparative analysis system. PMID:24165883
Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A. PMID:23811505
Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. PMID:23761787
Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. PMID:23755042
Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. PMID:23720654
The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. PMID:23653623
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. PMID:23628889
Improving microbial genome annotations in an integrated database context. PMID:23424620
Diversity of CRISPR systems in the euryarchaeal Pyrococcales. PMID:23422322
Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential. PMID:23409266
MetaMicrobesOnline: phylogenomic analysis of microbial communities. PMID:23203984
Learning virulent proteins from integrated query networks. PMID:23198735
CDD: conserved domains and protein three-dimensional structure. PMID:23197659
TIGRFAMs and Genome Properties in 2013. PMID:23197656
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. PMID:23165928
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. PMID:22966151
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4. PMID:22887663
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. PMID:22882546
Metagenomic annotation networks: construction and applications. PMID:22879885
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. PMID:22821013
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PMID:22792232
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains. PMID:22646228
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. PMID:22587810
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. PMID:22511878
Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. PMID:22354958
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. PMID:22194940
IMG: the Integrated Microbial Genomes database and comparative analysis system. PMID:22194640
The ins and outs of Mycobacterium tuberculosis protein export. PMID:22192870
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Nature and intensity of selection pressure on CRISPR-associated genes. PMID:22178975
CharProtDB: a database of experimentally characterized protein annotations. PMID:22140108
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
IMG/M: the integrated metagenome data management and comparative analysis system. PMID:22086953
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. PMID:22084572
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. PMID:22070167
Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. PMID:22037399
Genome shrinkage and loss of nutrient-providing potential in the obligate symbiont of the primitive termite Mastotermes darwiniensis. PMID:22020505
Genomic basis of endosymbiont-conferred protection against an insect parasitoid. PMID:21948522
TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. PMID:21886867
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. PMID:21878105
Evolutionary history and functional characterization of three large genes involved in sporulation in Bacillus cereus group bacteria. PMID:21821775
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. PMID:21742897
Genome sequence of Idiomarina sp. strain A28L, isolated from Pangong Lake, India. PMID:21742887
Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India. PMID:21742876
Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PMID:21738675
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. PMID:21725006
The oral metagenome in health and disease. PMID:21716308
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
HMMER web server: interactive sequence similarity searching. PMID:21593126
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PMID:21559529
Evolution and classification of the CRISPR-Cas systems. PMID:21552286
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. PMID:21478363
Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. PMID:21266540
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. PMID:21223593
1,000 structures and more from the MCSG. PMID:21219649
CDD: a Conserved Domain Database for the functional annotation of proteins. PMID:21109532
In silico gene expression analysis in Codonopsis lanceolata root. PMID:21088900
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PMID:20686689
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. PMID:20675471
Translational selection is ubiquitous in prokaryotes. PMID:20585573
SMURF: Genomic mapping of fungal secondary metabolite clusters. PMID:20554054
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. PMID:20500830
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. PMID:20411118
Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. PMID:20333224
MicroScope: a platform for microbial genome annotation and comparative genomics. PMID:20157493
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. PMID:20102603
Genetic tools for the investigation of Roseobacter clade bacteria. PMID:20021642
Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. PMID:19943115
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
The integrated microbial genomes system: an expanding comparative analysis resource. PMID:19864254
Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. PMID:19767433
FIGfams: yet another set of protein families. PMID:19762480
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families. PMID:19723314
The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PMID:19568419
The hedgehog signaling pathway: where did it come from? PMID:19564910
Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. PMID:19450243
webPRC: the Profile Comparer for alignment-based searching of public domain databases. PMID:19420063
A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifs. PMID:19383135
A bioinformatician's guide to metagenomics. PMID:19052320
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. PMID:19014591
FastBLAST: homology relationships for millions of proteins. PMID:18974889
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence. PMID:18705888
Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins. PMID:18658266
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
Modularity of stress response evolution. PMID:18495925
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases. PMID:18289380
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. PMID:18048332
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. PMID:17999997
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782 -
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
PubMed citations: 43.
43 articles citing: Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
Novel Plant Breeding Techniques Shake Hands with Cereals to Increase Production. PMID:35448780
Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis. PMID:33407096
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease. PMID:28585301
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem. PMID:28258138
A comprehensive software suite for protein family construction and functional site prediction. PMID:28182651
The landscape of microbial phenotypic traits and associated genes. PMID:27915291
Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections. PMID:26969701
Using comparative genomics to drive new discoveries in microbiology. PMID:25617609
TIGRFAMs and Genome Properties in 2013. PMID:23197656
Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PMID:23145189
Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. PMID:23046950
Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains. PMID:22646228
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. PMID:21223593
The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. PMID:21093452
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. PMID:20102603
The association of virulence factors with genomic islands. PMID:19956607
The comprehensive microbial resource. PMID:19892825
Pathema: a clade-specific bioinformatics resource center for pathogen research. PMID:19843611
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. PMID:19361336
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. PMID:19284550
The minimum information about a genome sequence (MIGS) specification. PMID:18464787
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
Replacement of the arginine biosynthesis operon in Xanthomonadales by lateral gene transfer. PMID:18305979
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases. PMID:18289380
Identification of genes encoding tRNA modification enzymes by comparative genomics. PMID:17673083
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. PMID:17420237
Computational approaches to phenotyping: high-throughput phenomics. PMID:17202287
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. PMID:17151080
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PMID:17112314
Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. PMID:16980487
Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. PMID:16980456
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. PMID:16930487
Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway. PMID:16901339
PROMPT: a protein mapping and comparison tool. PMID:16817977
Comparative genomics of NAD biosynthesis in cyanobacteria. PMID:16585762
Comparative genomics of emerging human ehrlichiosis agents. PMID:16482227
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. PMID:16381880
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PMID:16292354
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. PMID:16214803
Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. PMID:16159782 -
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes
PubMed citations: 13.
13 articles citing: Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes
Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning. PMID:35760985
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. PMID:34971560
Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes. PMID:34202069
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. PMID:34118976
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. PMID:33270901
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains. PMID:32214181
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics. PMID:31957879
GTP Preference of d-Glycero-α-d-manno-Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis. PMID:31906195
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Combinatorial Avidity Selection of Mosaic Landscape Phages Targeted at Breast Cancer Cells-An Alternative Mechanism of Directed Molecular Evolution. PMID:31454976
Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. PMID:31238501
A new genomic blueprint of the human gut microbiota. PMID:30745586
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computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
function analysis
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
homologous
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein-containing complex
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
proteome
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Tags
More detailed information about this field from each metasource.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
function analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genome annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
homologous
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein-containing complex
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
proteome
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome Properties; Genome Properties; DOI: https://doi.org/10.25504/FAIRsharing.A0ozDj; Last edited: Feb. 4, 2021, 2:47 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
computational predictions function analysis gene functional annotation genome genome annotation homologous protein-containing complex proteome sequence annotation
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