AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation ScienceHealth Care
Archaeal ProteinsRNA, ArchaealDNA, ArchaealGenes, ArchaealGenome, ArchaealGenomeArchaeaGenome, BacterialGenome, ViralArchaeal VirusesInfant FoodGene Expression Regulation, ArchaealGenome, HumanGenome, PlantPhylogenySulfolobusSequence Analysis, DNAGenome, MitochondrialMethanobacteriaceaeMethanococcalesCrenarchaeotaChromosomes, ArchaealMolecular Sequence DataEvolution, MolecularGenome, FungalBase SequenceMethanococcusSulfolobus solfataricusGenome SizeHaloferax volcaniiPyrococcus furiosusRibosome Subunits, Large, ArchaealGenomicsSequence AlignmentAmino Acid SequencePyrococcus abyssiGenome, InsectGenome, ProtozoanArchaeoglobus fulgidusBacteriaMethanosarcinaSulfolobus acidocaldariusPyrococcus horikoshiiOpen Reading FramesChromosome MappingGenome, ChloroplastSequence Homology, Amino AcidComputational BiologyAcidianusRNA, Ribosomal, 16SMethaneNanoarchaeotaPyrococcusDatabases, GeneticEuryarchaeotaConserved SequenceGene OrderThermoplasmaSoftwareGene Transfer, HorizontalSpecies SpecificityGenetic VariationSyntenyCloning, MolecularModels, GeneticMultigene FamilyEukaryotic CellsModels, MolecularGlyceryl EthersGeologic SedimentsGenome, HelminthDNA, BacterialThermoproteaceaeHuman Genome ProjectGenome, PlastidMethanobacteriumDNA, ViralNucleic Acid ConformationSequence Homology, Nucleic AcidMethanosarcinalesMolecular Sequence AnnotationDNA, RibosomalMutationRNA, TransferSeawaterMethanobacterialesTranscription, GeneticBacterial ProteinsBase CompositionRecombination, GeneticRibosome Subunits, Small, ArchaealEukaryotaProtein Structure, TertiaryGenes, BacterialInternetDesulfurococcaceaeGene DuplicationEscherichia coliPolymerase Chain ReactionBiodiversity
GenesBacterial genomesMicrobial GenomesProkaryoticSpeciesViralSequencesProteinGenomicMicrobiomeDatasetsAnnotationPhylogeneticPlastidMaritimusReplication originsMicrobesVirusesCrenarchaeotaRefSeqThaumarchaeotaSpecificityRevealsComputational methodsBiologyMetabolicGeneticPipelineReductionEvolutionaryCompleteSuccessfullyAnalysisHorizontal gene traSulfurTypeHostDiversityDatabasePublicationExtractTermsFeaturesPredictFound
Genes4
  • It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems. (biomedcentral.com)
  • This reduction resulted when genes from the endosymbiont's genome were transferred into the genome of the host organism. (reasons.org)
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
  • Our phylogenomic reconstruction (Figure 1) based on 122 archaeal single copy conserved marker genes (Parks et al. (uibk.ac.at)
Bacterial genomes3
  • For example, Lobry [ 3 ] employs the GC skew plot to predict replication origins and terminus in bacterial genomes. (biomedcentral.com)
  • The availability of hundreds of bacterial genomes allowed a comparative genomic study of the Type VI Secretion System (T6SS), recently discovered as being involved in pathogenesis. (biomedcentral.com)
  • They see the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles. (reasons.org)
Microbial Genomes1
  • This genome was automatically retrieved and processed using MiGA (The Microbial Genomes Atlas) [1] , and the estimate has not been overridden by the submitter. (uibk.ac.at)
Prokaryotic6
  • RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms. (nih.gov)
  • We are embarking on this adventure and starting to place terms from the Biological Process, Molecular Function and Cellular Component ontologies to genomes and proteins we annotate with the Prokaryotic Genome Annotation Pipeline (PGAP). (nih.gov)
  • Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. (biomedcentral.com)
  • We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. (biomedcentral.com)
  • The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. (biomedcentral.com)
  • By combining comparative and phylogenetic approaches using more than 500 prokaryotic genomes, we characterized the global T6SS genetic structure in terms of conservation, evolution and genomic organization. (biomedcentral.com)
Species4
Viral1
  • Real-time reverse transcription-polymerase chain reaction (RT-PCR), viral whole genome sequencing, and viral culture was performed on these nasal specimens. (cdc.gov)
Sequences6
  • This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences that have been assembled, annotated and deposited in public databases. (wikipedia.org)
  • MTase methylates specific DNA sequences (recognition sites) in the host genome. (biomedcentral.com)
  • Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. (cam.ac.uk)
  • 7 ] develop the Oriscan algorithm to predict replication origins in the S. cerevisiae genome by searching for sequences similar to a training set of 26 known yeast origins pinpointed by site-directed mutagenesis. (biomedcentral.com)
  • Dr. Roberts gave this interesting simile that getting more and more DNA sequences of bacteria is like getting a car with a list of all its parts with no idea about how they fit together or how they work. (egybio.net)
  • Determine the two most related and two least related organisms from a short list of 16S rRNA sequences. (qubeshub.org)
Protein3
  • See the KatG protein found in many Klebsiella genomes in Figure 2. (nih.gov)
  • This genome wide analysis allowed the identification of a set of 13 proteins constituting the T6SS protein core and a set of conserved accessory proteins. (biomedcentral.com)
  • Satellite viruses replicating in plants have small icosahedral virions and encapsidate positive-sense RNA genomes typically carrying a single gene for the capsid protein. (hal.science)
Genomic2
  • The genome of the type strain was sequenced as part of the GEBA (Genomic Encyclopedia of Bacteria and Archaea ) project. (dsmz.de)
  • Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? (biomedcentral.com)
Microbiome1
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
Datasets2
  • Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. (peerj.com)
  • Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes. (peerj.com)
Annotation4
  • Figure 1: Excerpt from the RefSeq record for NZ_CP091650.1 , a Klebsiella pneumoniae genome, showing the annotation of the the katG gene, with Molecular Function GO terms GO:0004096 and GO:0004601 and Biological Process GO term GO:0006979 . (nih.gov)
  • Here, we report a GEM reconstruction for strain SCM1 based on this genome annotation information (Walker et al. (springeropen.com)
  • The long-term objective of this STTR project is to develop a semantic index of bacterial and archaeal phenotypes that can be used to augment annotation efforts and to provide a basis for predictive modeling of microbial phenotype. (namesforlife.com)
  • Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). (theseed.org)
Phylogenetic1
  • List the three Domains of the phylogenetic tree of life. (qubeshub.org)
Plastid1
  • 2014. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. (nih.gov)
Maritimus2
  • Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. (ouhsc.edu)
  • Here, based on the published genome of Nitrosopumilus maritimus SCM1, a genome-scale metabolic model named NmrFL413 was reconstructed. (springeropen.com)
Replication origins4
  • A number of computational methods have been developed for predicting replication origins in bacterial, archaeal, and eukaryotic genomes. (biomedcentral.com)
  • 4 ] predict the replication origins for a number of bacterial and archaeal genomes by identifying some 7-mers and/or 8-mers whose orientation is preferentially skewed around the replication origins. (biomedcentral.com)
  • Zhang and Zhang [ 5 ] use the Z-curve method successfully to identify several replication origins in bacterial and archaeal genomes. (biomedcentral.com)
  • If you want to predict the replication origin in the genome, you can use web servers developed by our lab: Ori-Finder 2022 ( http://tubic.tju.edu.cn/Ori-Finder/ and https://tubic.org/Ori-Finder/ ), a tool for predicting bacterial replication origins, and Ori-Finder 2 ( http://tubic.tju.edu.cn/Ori-Finder2/ ), a tool for predicting archaeal replication origins. (tubic.org)
Microbes3
  • These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. (peerj.com)
  • After joining the JGI, he formed the Microscale Applications group to operate a similar single-cell genomics pipeline that provides JGI users access to the genomes of uncultured microbes. (doe.gov)
  • According to this idea, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a "host" microbe. (reasons.org)
Viruses3
  • Thus, for genome replication these viruses necessarily depend on helper viruses which can belong to different families. (hal.science)
  • 15-) using a local database for identification of all viruses, bacteria and archaeal genomes extracted from the NCBI refseq database (downloaded 15/04/2017). (cdc.gov)
  • The resulting contigs were scanned against several BLAST ( 12 ) pre-generated databases downloaded from NCBI ( nt , tsa_nt , ref_prok_rep_genomes , ref_viruses_rep_genomes , and vector - downloaded 15/04/2017). (cdc.gov)
Crenarchaeota2
RefSeq3
  • Bacterial and archaeal genomes with GO terms in RefSeq! (nih.gov)
  • They will progressively appear on genomes that are already in RefSeq as these get reannotated (about once a year). (nih.gov)
  • We expect all RefSeq genomes to have some GO terms by the spring of 2023. (nih.gov)
Thaumarchaeota2
  • Although a total of 70 thaumarchaeotal genomes were published up to now, no GEM has been reconstructed for microorganisms in the phylum Thaumarchaeota , which is a major impediment for a comprehensive study of evolution and diversity in archaea. (springeropen.com)
  • The genome of SCM1, representing the most abundant marine Thaumarchaeota , was published in 2010 (Walker et al. (springeropen.com)
Specificity1
  • Because of the hierarchical nature of the Gene Ontologies, these annotations will help the comparison of gene content across genomes at variable levels of specificity and eventually allow GO term enrichment analysis. (nih.gov)
Reveals1
  • Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. (ebsco.com)
Computational methods2
  • R-M systems are widely spread among prokaryotes: they have been found or predicted with computational methods in the vast majority of bacterial and archaeal genomes [ 13 ]. (biomedcentral.com)
  • Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. (biomedcentral.com)
Biology1
Metabolic1
  • In recent years, genome-scale metabolic models (GEMs) have been developed for quantitative prediction of intracellular metabolic flux distributions based on mass balance constraints coined in the stoichiometric matrix of a metabolic model. (springeropen.com)
Genetic1
  • The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA. (ouhsc.edu)
Pipeline1
  • We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. (peerj.com)
Reduction1
  • Presumably, the endosymbiont gradually evolved into an organelle through a process referred to as genome reduction. (reasons.org)
Evolutionary2
  • Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle's evolutionary history. (reasons.org)
  • List two features of a useful molecular/evolutionary clock. (qubeshub.org)
Complete1
Successfully1
  • Tips for a Winning Community Science Program Proposal In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program. (doe.gov)
Analysis1
  • With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. (theseed.org)
Horizontal gene tra1
Sulfur1
  • The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C". Archaea. (wikipedia.org)
Type1
  • The index is based on published descriptions of taxonomic type and non-type strains that have been the subject of ongoing genome sequencing efforts as this will provide a mechanism whereby hypotheses can be tested and reproducibility verified. (namesforlife.com)
Host1
  • The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. (biomedcentral.com)
Diversity1
  • Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. (peerj.com)
Database2
  • We are working to add GO terms on more hidden Markov models (HMMs) and BlastRules as well as Conserved Domain Database (CDD) architectures, so that a larger proportion of the gene content of each genome can inherit GO terms. (nih.gov)
  • You can input a DoriC accession number list to search oriC maps recorded in DoriC database for comparison. (tubic.org)
Publication1
  • The SeqCode was notified on 2023-08-23 of effective publication of this name, as part of the register list seqco.de/r:0qcnd580 . (uibk.ac.at)
Extract1
  • In this chapter, we give a brief historical overview of the knowledge gained from P. aeruginosa genome sequencing, then we describe the wet-lab procedure to extract the DNA and prepare the library for broad genome sequencing using Illumina MiSeq technology. (bvsalud.org)
Terms1
  • GO terms are now associated with coding sequence (CDS) features on newly-submitted genomes (See Figure 1). (nih.gov)
Features1
  • In total, 41% of CDS features on this genome have at least one GO term. (nih.gov)
Predict1
Found2
  • We also found cases of site avoidance in absence of the corresponding R-M systems in the genome. (biomedcentral.com)
  • A list of our current non-bibliographic LinkOut providers can be found here . (nih.gov)