• U57694 Microglena monadina strain SAG 31.72 18S small subunit ribosomal RNA gene, partial sequence. (uni-goettingen.de)
  • Here, we reanalyze the small-subunit ribosomal RNA gene (SSU rDNA) phylogeny by removing all long-branching lineages that could artifactually attract foraminiferan sequences to the base of the tree. (unige.ch)
  • Collection of small (16S and 16S-like) subunit ribosomal RNA structures: 1994. (microbiologyresearch.org)
  • Field and microscopic observations of the 3 pathogens are complemented by the first E. dicksonii large subunit ribosomal RNA (LSU rRNA) gene sequence analyses of isolates from Lesvos and other parts of the world. (elsevierpure.com)
  • The services are applied to study the phylogeny, taxonomy and diversity from complex microbiomes. (rapidmicrobiology.com)
  • The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. (scienceopen.com)
  • This feature is particularly useful for comparing phylogeny with taxonomy when dealing with thousands of genomes. (scienceopen.com)
  • These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus. (mcmaster.ca)
  • Microbial whole genome sequencing is a critical approach for sequencing the entire genomes of bacteria, fungi, viruses and other microbes. (rapidmicrobiology.com)
  • This new implementation attempts to meet the challenge of ever increasing amount of genome data and includes in its database more than 850 prokaryotic genomes which will be updated monthly from NCBI, and more than 80 fungal genomes collected manually from several sequencing centers. (scienceopen.com)
  • Since the first bacterial genomes were sequenced in 1995 there have been several attempts to infer prokaryote phylogeny from complete genomes. (scienceopen.com)
  • Sequencing the entire bacterial genome is important for generating accurate reference genomes, microbial identification, and other comparative studies. (cd-genomics.com)
  • Microbial whole-genome de novo sequencing is an important tool for mapping genomes of novel organisms, whereas microbial whole-genome resequencing investigates genomes of known organisms, or comparing genomes across multiple samples. (cd-genomics.com)
  • With the ability to capture the whole picture of microbial genetic information, metagenomic sequencing also provides the approach to understand the functions encoded by the genomes of the microbiome, which contains bacteria, archaea, and fungi. (cd-genomics.com)
  • Still, as the DNA sequences of complete genomes have become increasingly available, research groups have noticed patterns that are disturbingly at odds with the prevailing beliefs. (biologyjunction.com)
  • Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. (cdc.gov)
  • There were 336 sequence types (STs) among the 1,019 sequenced genomes, and the genomes varied by an average of 84.7% of the cgMLST alleles used. (cdc.gov)
  • The development of whole genome-based alignment-free CV method has provided an independent verification to the traditional phylogenetic analysis based on a single gene or a few genes. (scienceopen.com)
  • The development of next-generation sequencing (NGS) technologies allows researchers to investigate microorganisms from a broader and deeper perspective, enabling better characterization of the bacterial genome as well as deeper taxonomic identification of complex microbiomes in specific environments such as soil, ocean, and even human body. (cd-genomics.com)
  • Whole genome sequencing is an unbiased approach for bacterial profiling. (cd-genomics.com)
  • In addition to genes, there are many other functional parts of the genome. (blogspot.com)
  • Scientists know what they are talking about when they say that the human genome contains about 20,000 protein-coding genes and at least 5,000 genes for non-coding RNAs. (blogspot.com)
  • They are comfortable with the idea that our genome has lots of other functional regions that lie outside of the genes. (blogspot.com)
  • Then they confuse themselves by thinking that knowledgeable experts use the word "gene" as a synonym for all functional sequences in the genome. (blogspot.com)
  • To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. (mcmaster.ca)
  • Sequence variability at ospC is the highest among known genomic loci and is strongly linked to variations at other genome-wide loci, with occasional recombinant genotypes caused by plasmid exchanges ( 16 - 19 ). (cdc.gov)
  • We performed AST and whole genome sequencing (WGS) for 593 C. difficile isolates collected between 2012-2017 through the Centers for Disease Control and Prevention's Emerging Infections Program. (cdc.gov)
  • Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC's Emerging Infections Program, United States, 2016-2018. (cdc.gov)
  • To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. (cdc.gov)
  • Phylogenetic position of the subgenus Lordiphosa of the genus Drosophila (Diptera: Drosophilidae) inferred from alcohol dehydrogenase (Adh) gene sequences. (wikipedia.org)
  • Internal transcriber spacer (ITS) sequences and several chloroplast markers, rpoB , rpoC1 , and psbA-trnH were sequenced in order to infer a preliminary phylogeny of the genus. (bioone.org)
  • Until supplemental phenotypic traits become available, the genus 'Candidatus Phytoplasma', is designated, on the basis of phylogeny, as a tentative member in the family Acholeplasmataceae. (usda.gov)
  • The phylogenetic analyses based on a combined LSU, ITS, SSU, and TEF1-α sequence data showed that the new collections are affiliated with the genus Fissuroma and can be recognized as a new species Fissuroma bambusicola . (mapress.com)
  • Index fungorum ( http://www.indexfungorum.org/ ) lists 17 species names under this genus, but molecular phylogenies have reduced the number to ten (Zhao et al. (biomedcentral.com)
  • Using a variety of phylogenetic methods, 18S rRNA phylogenies indicate that the genus Trypanosoma is not monophyletic. (biomedcentral.com)
  • By contrast, phylogenetic analyses of available sequences in 42 protein families gene generally supported monophyly of the genus Trypanosoma . (biomedcentral.com)
  • 1996) Phylogeny of the Chlamydomonadales (Chlorophyceae): A Comparison of Ribosomal RNA Gene Sequences from the Nucleus and the Chloroplast. (uni-goettingen.de)
  • EF113423 rbcL gene, partial cds, chloroplast. (uni-goettingen.de)
  • This study represents phylogenetic analyses of two woody polygonaceous genera Calligonum and Pteropyrum using both chloroplast fragment (trnL-F) and the nuclear ribosomal internal transcribed spacer (nrDNA ITS) sequence data. (ijbiotech.com)
  • To clarify the monophyly and phylogenetic position of the species, a molecular study using the internal transcribed spacer region of nuclear ribosomal DNA and chloroplast DNA ( trn L-F) data was conducted. (e-kjpt.org)
  • 16S/18S/ITS amplicon metagenomic sequencing is designated to sequence the target genes of 16S ribosomal RNA (rRNA), or 18S rRNA and Internal Transcribed Spacer (ITS) by universal primers. (rapidmicrobiology.com)
  • Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. (anthropogeny.org)
  • Shotgun metagenomic sequencing overcomes many limitations of the amplicon sequencing . (cd-genomics.com)
  • Shotgun metagenomic sequencing produces vast amounts of data that can be analyzed by powerful computing technologies. (cd-genomics.com)
  • Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases. (cd-genomics.com)
  • These loci (rrnA, rrnB and rrnC) were isolated on recombinant lambda clones, and comprised 16S, 23S and 5S rRNA genes closely linked in that order. (microbiologyresearch.org)
  • Higher sections of the universal tree of life have based many of their branching patterns on sequence analysis of rRNA genes. (biologyjunction.com)
  • We will show that phylogenies based on 18S ribosomal RNA (18S rRNA) genes have provided an answer to this question that appears inconsistent with the results of the majority of phylogenies based on available protein sequences. (biomedcentral.com)
  • Twenty-nine strains (representing 79% of the complete collection) were further identified by 16S rRNA gene sequencing, rpoB gene sequencing and DNA-DNA hybridizations. (ilvo.be)
  • The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii, in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. (nih.gov)
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
  • Diversity, Phylogeny, anticancer and antimicrobial potential of fungal endophytes associated with Monarda citriodora L. (biomedcentral.com)
  • demonstrated that great variations in chromosome numbers are associated with rapid species diversity due to agmatoploidy (chromosome number increases by fission without gene duplications) ( Luceño and Guerra, 1996 ) and/or aneuploidy in various linages. (e-kjpt.org)
  • Metatranscriptome sequencing has provided significant insights about the microbial community structure and functional characterization of the complex metabolic interactions within a single microbiome, which help to elucidate key genes and pathways, discover gene activity diversity, and conduct gene expression comparison. (cd-genomics.com)
  • A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries. (wikipedia.org)
  • Genomic organisation of the neural sex determination gene fruitless (fru) in the Hawaiian species Drosophila silvestris and the conservation of the fru BTB protein-protein-binding domain throughout evolution. (wikipedia.org)
  • Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: a nuclear versus mitochondrial gene approach. (wikipedia.org)
  • nucleotide hydrogenase subunit 1 gene (NAD1) and The morphologic, taxonomic, and molecular cytochrome c oxidase subunit 1 gene (COX1), and 3 analysis of several species classified in the family An- nuclear ribosomal markers, the second internal tran- oplocephalidae are not well documented ( 6 ). (cdc.gov)
  • 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. (biomedcentral.com)
  • To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. (anthropogeny.org)
  • We also described the phylogenetic relationships among these species which were analyzed using ribosomal RNA and other gene sequences. (usda.gov)
  • Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. (bvsalud.org)
  • METHODS AND RESULTS: The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. (bvsalud.org)
  • It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. (bvsalud.org)
  • Eleven species including Calligonum (6 species), Pteropyrum (3 species) and Atraphaxis (2 species) were sequenced for both regions newly. (ijbiotech.com)
  • This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. (nih.gov)
  • Species from these clades also generally grouped together in 16S rRNA gene trees. (mcmaster.ca)
  • In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. (mcmaster.ca)
  • One possible explanation for these conflicting results is poor taxon sampling in the case of protein coding genes, most of which have been sequenced for only a few species of Trypanosomatidae. (biomedcentral.com)
  • However, sequences from only a relatively small number of species were available at the time of this analysis. (biomedcentral.com)
  • Since theses species are unquestioned outgroups to both Trypanosomatidae and Bodonidae, the phylogeny of Wright et al. (biomedcentral.com)
  • MLST studies showed that local populations of a bacterial species typically consist of discrete clusters of multilocus sequence types called "clonal complexes," rather than a multitude of randomly assorted genotypes ( 2 ). (cdc.gov)
  • DNA extraction, amplification, and sequencing: Total genomic DNA was isolated from dried leaf or branchlet (only for Calligonum) of samples using the modified cetyl trimethylammonium bromide (CTAB) method of Doyle and Doyle (1987). (ijbiotech.com)
  • Compared with Sanger sequencing based on selective binding chain-terminating dideoxynucleotides during in vitro replication by DNA polymerase, NGS has high sequencing depth, which allows for high sensitivity and comprehensive genomic coverage. (cd-genomics.com)
  • Assigning amplicon sequences to operational taxonomic units (OTUs) is an important step in characterizing microbial communities across large data sets. (nih.gov)
  • 16S rRNA amplicon sequencing, metagenomics, and metatranscriptomics are widely used NGS strategies in bacterial identification and characterization. (cd-genomics.com)
  • Efficient and robust software tools are needed to assign microbial sequences into taxonomic groups for characterization and comparison of communities. (nih.gov)
  • Phylogenetic analysis based on gene sequences, in particular, ribosomal sequences, has provided the major supporting evidence for the composition and taxonomic subdivision of this group of organisms with diverse habitats and ecology and has become the mainstream for the Acholeplasmataceae systematics. (usda.gov)
  • 16S ribosomal RNA sequencing has been used extensively in bacterial phylogeny and the taxonomic composition of a microbiome. (cd-genomics.com)
  • Molecular phylogeny of the mitochondrial markers in a study of Bertiella tapeworms in children in Sri Lanka. (cdc.gov)
  • Recognizing this, we developed a novel risk signature based on mitochondrial-related genes to improve prognosis prediction and risk stratification in breast cancer patients. (bvsalud.org)
  • The mitochondrial genes MT-ATP6 and MT-ATP8 encode two subunits of the multi-subunit Complex V. Since the discovery of the first MT-ATP6 variant in the year 1990 as the cause of Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome, a large and continuously increasing number of inborn variants in the MT-ATP6 and MT-ATP8 genes have been identified as pathogenic. (bvsalud.org)
  • In the present review, we report the pathogenic variants in mitochondrial ATP synthase genes and highlight the molecular mechanisms underlying ATP synthase deficiency that promote biochemical dysfunctions. (bvsalud.org)
  • Finally, we provide the state-of-the-art of all therapeutic proposals reported in the literature, including drug interventions targeting mitochondrial dysfunctions, allotopic gene expression- and nuclease-based strategies, and discuss their potential translation into clinical trials. (bvsalud.org)
  • These elements included a single promoter, which was mapped upstream of the 16S rRNA gene and which was similar to Escherichia coli consensus promoter sequences, an AT-rich upstream region, a GC-rich motif that may be involved in stringent control, leader and spacer antitermination sequences, sites for ribonuclease processing, and a putative factor-independent terminator sequence. (microbiologyresearch.org)
  • Boros I. , Csordés-Tôth E. , Kiss A. , Tôrôk I. , Udvardy K. , Venetianer P. Identification of two new promoters probably involved in the transcription of a ribosomal RNA gene of Escherichia coli. (microbiologyresearch.org)
  • Brosius J. , Dull D.J. , Sleeter D.D. , Noller H.F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. (microbiologyresearch.org)
  • Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). (cmich.edu)
  • To resolve phylogenetic relationships among isolates, we sequenced 68 isolates from Europe and North America at 1 chromosomal locus (16S-23S ribosomal RNA spacer) and 3 plasmid loci ( ospC , dbpA , and BBD14). (cdc.gov)
  • The ospC -A clone appeared to be highly prevalent on both continents, and isolates of this clone were uniform in DNA sequences, which suggests a recent trans-oceanic migration. (cdc.gov)
  • The genetic homogeneity of ospC -A isolates was confirmed by sequences at 6 additional chromosomal housekeeping loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)
  • WGS was performed on all isolates to detect the presence of genes or mutations previously associated with resistance. (cdc.gov)
  • RT027 isolates also showed higher MICs to clindamycin and moxifloxacin and were more likely to harbor associated resistance genes or mutations. (cdc.gov)
  • While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase -lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. (cdc.gov)
  • The increased carbapenem resistance in isolates with acquired non-carbapenemase -lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa. (cdc.gov)
  • Multilocus sequence typing (MLST) is the use of DNA sequences at multiple housekeeping loci to characterize genetic variations of natural populations of a bacterial pathogen ( 1 , 2 ). (cdc.gov)
  • Recently, a multilocus sequence analysis approach was proposed to reconstruct phylogenetic histories of bacterial clonal complexes by using concatenated sequences of housekeeping genes when within-loci and between-loci recombinations are infrequent ( 5 ). (cdc.gov)
  • Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses. (wikipedia.org)
  • Our analyses reveal that Foraminifera branch together with the marine testate filosean Gromia oviformis as a sister group to Cercozoa, in agreement with actin phylogeny. (unige.ch)
  • Phylogenetic analyses of the family Trypanosomatidae have been conducted using both 18S rRNA gene sequences and a variety of protein sequences. (biomedcentral.com)
  • Promputtha, I. (2015) The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. (mapress.com)
  • Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene. (wikipedia.org)
  • Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support. (wikipedia.org)
  • A) Maximum-likelihood tree containing 25 taxa constructed by the analysis of partial NAD1 sequence alignment. (cdc.gov)
  • B) Maximum-likelihood tree containing 37 taxa was constructed by the analysis of partial COX1 sequence alignment. (cdc.gov)
  • Identification was performed by sequencing 18S rRNA that was compared with known genes using Blast search in the combination of phylogenic analysis by using Clustal W and PhyML in GenomeNet. (microbiologyjournal.org)
  • An overview of the different applications of next-generation sequencing analysis. (cd-genomics.com)
  • Sequence and primer extension analysis revealed the presence of putative genes encoding tRNA lle and tRNA Ala within the 16S-23S spacer region, as well as a number of potential regulatory features. (microbiologyresearch.org)
  • Baylis H.A. , Bibb M.J. Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomjces A3(2). (microbiologyresearch.org)
  • The advent of molecular sequence data provided many additional characters for phylogenetic analysis, but so far evolutionary relationships within the family remain poorly resolved even by molecular data [ 1 - 7 ]. (biomedcentral.com)
  • Here we include new sequences of Myrrhinium atropurpureum in a comprehensive molecular phylogeny based on a balanced sample of two plastid and two nuclear markers, with the aim of providing the historical framework of pollination by frugivorous birds in Myrteae. (peerj.com)
  • sequence similarity search identified infecting humans ( 9 ). (cdc.gov)
  • These mutations define genes that are known to act in genetic regulatory hierarchies controlling pattern formation, differentiation, and morphogenesis. (nyu.edu)
  • With the recognition that DNA was the genetic material, the word "gene" took on an additional meaning as a physical unit of function. (blogspot.com)
  • In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. (rsc.org)
  • In addition to the host regulatory mechanisms response to disease, the microbiome can make changes to the expression of the host features such as their genes, proteins, and/or PTMs. (rsc.org)
  • A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies. (cd-genomics.com)
  • All inferred phylogenies using parsimony and Bayesian methods showed that Calligonum and Pteropyrum are both monophyletic and closely related taxa. (ijbiotech.com)
  • In the present work, the evolutionary changes producing these differences were reconstructed in the context of the four possible phylogenies supported independently by sequences of 18S ribosomal RNA genes (rDNA). (nyu.edu)
  • however, when combined with the rDNA characters, they provide stronger support for one of the four rDNA phylogenies. (nyu.edu)
  • Our study confirms the utility of SSU rDNA as a phylogenetic marker of megaevolutionary history, provided that the artifacts due to the heterogeneity of substitution rates in ribosomal genes are circumvented. (unige.ch)
  • By relating the steps of male tail morphological evolution to the phenotypic changes brought about by developmental mutations induced experimentally in C. elegans, the goal is to identify genes responsible for morphological evolution. (nyu.edu)
  • The lack of vanA/B genes or mutations consistently associated with elevated vancomycin MICs suggests there are multifactorial mechanisms of resistance. (cdc.gov)
  • skeletal abnormalities and gene mutations are not a requirement to confirm the diagnosis. (medscape.com)
  • In 90% of cases, SDS is associated with mutations in the Shwachman-Bodian-Diamond syndrome ( SBDS ) gene, located on chromosome 7. (medscape.com)
  • Also, Shwachman-Diamond syndrome has been associated with mutations in the SBDS gene, located on chromosome 7. (medscape.com)
  • 2012) Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales. (uni-goettingen.de)
  • The problem with this part of the book (the part about the molecular gene) is that the authors seem to be confused about the difference between a molecular gene and the view that "genes" are the only thing that count in genetics, evolution, metabolism etc. (blogspot.com)
  • Finally, they misunderstand the term "gene-centric" where the word "gene" is used metaphorically to refer to any DNA sequence that functions in population genetics and evolution. (blogspot.com)
  • Environmental sequences of ten novel plastid lineages and structural innovations in plastid proteins confirm that plastids in apicomplexans and their relatives are widespread and share a common, photosynthetic origin. (elifesciences.org)
  • The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. (rsc.org)
  • They seem to think that the gene-centric view requires that everything be attributed to DNA sequences that encode proteins. (blogspot.com)
  • They proposed basing family trees on differences in the building block sequences for genes and proteins. (biologyjunction.com)
  • Their approach is known as molecular phylogeny, and it states that individual genes are composed of unique sequences of nucleotides that typically serve as the blueprint for making specific proteins. (biologyjunction.com)
  • DNA sequences encoding 2 essential cellular proteins agreed that the last common ancestor spawned both the true bacteria and archaic bacteria and then the eukaryotes (with a nucleus) branched from the archaic. (biologyjunction.com)
  • Berg K.L. , Squires C. , Squires C.L. Ribosomal RNA operon anti-termination Function of leader and spacer region box B-box A sequences and their conservation in diverse microorganisms. (microbiologyresearch.org)
  • Sanchez and Kron (2008) using cpDNA sequences (rbcL and matK), and then Sanchez et al. (ijbiotech.com)
  • The key features of NGS include in vitro library construction and clonal amplification, array-based sequencing enables DNA fragments to be multiplexed, and DNA solid-phase fixation. (cd-genomics.com)
  • Eventually the bacterium gave up its ability to live on its own and transferred some of its genes to the nucleus of the host becoming a mitochondrion. (biologyjunction.com)
  • Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. (scienceopen.com)
  • The composition vector method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. (scienceopen.com)
  • Transcription is controlled by regulatory sequences such as promoters, operators, and enhancers but these are not part of the gene. (blogspot.com)
  • A notable difference between de novo clustering and database-dependent reference clustering methods is that OTU assignments from de novo methods may change when new sequences are added. (nih.gov)
  • Existing reference-based methods produce consistent OTUs but only consider the similarity of each query sequence to a single reference sequence in an OTU, resulting in assignments that are worse than those generated by de novo methods. (nih.gov)
  • Inspired by the de novo OptiClust algorithm, OptiFit considers the similarity of all pairs of reference and query sequences to produce OTUs of the best possible quality. (nih.gov)
  • These differences, made apparent when calculating ribosomal RNA:DNA ratios, have been interpreted as variable activities of bacterial populations. (doe.gov)
  • IMPORTANCE Advancements in DNA sequencing technology have allowed researchers to affordably generate millions of sequence reads from microorganisms in diverse environments. (nih.gov)
  • The remaining sequences were obtained from GenBank. (ijbiotech.com)