• Our technique takes advantage of the atomic force microscope's (AFM) ability to detect piconewton scale forces in order to read off sequencing information based on the interaction of nucleotides with a cyclodextrin. (nsti.org)
  • The resulting product is treated with ExoSAP-IT™, prior to sequencing, to degrade the unincorporated primers and hydrolyze the free nucleotides. (thermofisher.com)
  • Obvious reasons for preferential realization of pairing phase 3 are the elevated GC content and the near equi- valent frequencies of base pairing nucleotides (A C25 U, C C25 G) at the third codon site, relative to other sites (Supplementary Table 1). (psu.edu)
  • Shuffling of nucleotides at the third synonymous codon sites which retained nucleotide composi- tion and amino acid sequence of the native mRNAs affected nucleotide base pairing to some extend due to changes in codon context (Table 1). (psu.edu)
  • further explanation needed] They proposed that these ribosomal nucleotides recognize the complementary purine-rich sequence AGGAGGU, which is found upstream of the start codon AUG in a number mRNAs found in viruses that affect E. coli. (wikipedia.org)
  • Each template cluster undergoes sequencing-by-synthesis in parallel using novel fluorescently labelled reversible terminator nucleotides. (wikipedia.org)
  • Visual motion is one of the most important cues for the interpretation of image sequences. (bl.uk)
  • Research interest has naturally focused on the development of techniques that enable arbitrary image sequences to be efficiently decomposed into their constituent layers. (bl.uk)
  • The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen. (nih.gov)
  • Furthermore, the genomic compartment in which the markers reside might affect the diversity pattern seen, and it is possible that markers residing mainly in junk DNA might produce different results from markers based upon genes, which are predominantly euchromatic. (genetics.org)
  • MLST and SLST analyze essential protein coding genes, or housekeeping genes, that encode for proteins necessary for the normal cellular functions of the bacterium all of which contain more variability in their sequences. (criver.com)
  • Both the NGS platform and Oncomine reagents leverage the Ion AmpliSeq technology, which enables simultaneous sequencing of hundreds of genes, with high reproducibility and rapid turnaround time. (businesswire.com)
  • Employing the topological features in the protein interaction network and the sequence properties, we have built a machine learning classifier capable of predicting essential genes . (rsc.org)
  • in Escherichia coli, for example, the sequence is AGGAGGU, while subsequence GAGG dominates in E. coli virus T4 early genes. (wikipedia.org)
  • THE genetic diversity of a species is the sum of its total DNA sequence variation, resulting from millions of years of cumulative mutation, recombination, and selection. (genetics.org)
  • Attributes containing sets or sequences of elements appear in various application domains, e.g. in telecommunication and retail databases, multimedia systems, web server logs, genetic and molecular databases, etc. (psu.edu)
  • Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. (nih.gov)
  • The guidances provide recommendations for designing, developing, and validating tests that use the technology, called next generation sequencing (NGS), and will play an important role in the continued advancement of individualized, genetic-based medicine. (fda.gov)
  • The first guidance issued today, " Use of Public Human Genetic Variant Databases to Support Clinical Validity for Genetic and Genomic-Based In Vitro Diagnostics ," describes an approach where test developers may rely on clinical evidence from FDA-recognized public databases to support clinical claims for their tests and help provide assurance of the accurate clinical evaluation of genomic test results. (fda.gov)
  • The second guidance issued today, " Considerations for Design, Development, and Analytical Validation of Next Generation Sequencing (NGS)-Based In Vitro Diagnostics (IVDs) Intended to Aid in the Diagnosis of Suspected Germline Diseases ," provides recommendations for designing, developing, and validating NGS-based tests used to diagnose individuals with suspected genetic diseases. (fda.gov)
  • In 2017, the FDA took several actions to streamline the development and review of a variety of genetic-based tests - authorizing a third-party option for conducting reviews NGS tumor profiling tests and making clearance recommendations to FDA , as well as outlining standardized development criteria for carrier screening tests to allow for their marketing without prior agency review. (fda.gov)
  • Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. (nih.gov)
  • If the 16S sequence is different, you can be sure that the isolates are different strains. (criver.com)
  • The portal, which launched with an initial 250 genome sequences of widely used bacterial strains, delivers on ATCC's Enhanced Authentication Initiative , a component of the first of five core pledges under the Incredible 2020 Initiative aimed at increasing reproducibility in biological research. (atcc.org)
  • Since then, sequencing has shown the presence of several mutations in the few available clinical strains compared to the sequence of the type strain M. genitalium G37 ( 13 ). (asm.org)
  • We determined the discriminatory index (DI), i.e., the likelihood that unrelated strains sampled from the test population would be placed into different typing groups ( 10 ), by sequencing specimens from unrelated patients. (asm.org)
  • In particular, we examine the possibility of jointly base-calling two superposed DNA sequences by applying the sum-product algorithm on factor graphs. (mit.edu)
  • Bennett Fox, Algorithm 647: Implementation and Relative Efficiency of Quasirandom Sequence Generators, ACM Transactions on Mathematical Software, Volume 12, Number 4, pages 362-376, 1986. (fsu.edu)
  • Applying the particle filter (PF) technique, this paper proposes a PF-based algorithm to blindly demodulate the chaotic direct sequence spread spectrum (CDS-SS) signals under the colored or non-Gaussian noises condition. (mdpi.com)
  • Simulations show that the proposed PF-based algorithm can obtain a good bit-error rate performance when extracting the original binary message from the CDS-SS signals without any knowledge of the transmitter's chaotic map, or initial value, even when colored or non-Gaussian noises exist. (mdpi.com)
  • For music retrieval, the authors use the Smith-Waterman (SW) algorithm to measure the similarity between mood sequences. (igi-global.com)
  • When provided with two sequences from the same subject and one from a different subject, an algorithm identifies the foreign sequence in up to 88% of the cases. (ebscohost.com)
  • The Shine-Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon. (wikipedia.org)
  • In 1973 Dalgarno and Shine proposed that in eukaryotes, the 3'-end of the small 18S rRNA may play a role in the termination of protein synthesis by complementary base pairing with termination codons. (wikipedia.org)
  • Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it was proposed to have a role in the termination of protein synthesis in eukaryotes. (wikipedia.org)
  • ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. (wikipedia.org)
  • ChIP is a powerful method to selectively enrich for DNA sequences bound by a particular protein in living cells. (wikipedia.org)
  • Oligonucleotide adaptors are then added to the small stretches of DNA that were bound to the protein of interest to enable massively parallel sequencing. (wikipedia.org)
  • Compared to ChIP-chip, ChIP-seq data can be used to locate the binding site within few tens of base pairs of the actual protein binding site. (wikipedia.org)
  • A single sequencing run can scan for genome-wide associations with high resolution, meaning that features can be located precisely on the chromosomes. (wikipedia.org)
  • Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. (genetics.org)
  • All the sequences from each gene target are aligned and compared to the other organisms' sequence data and the level of divergence or conservation between the organisms is calculated and displayed with a phylogenetic tree. (criver.com)
  • We will interpret the data for you and state whether the isolates are indistinguishable by the sequencing of the particular gene targets or whether the isolates are different sequence types. (criver.com)
  • In addition, we have also examined sequence properties such as open reading frame length, strand, and phyletic retention for their association with the gene essentiality. (rsc.org)
  • Gabel C, Maier R. Nucleotide sequence of the coxA gene encoding subunit I of cytochrome aa3 of Bradyrhizobium japonicum. (labome.org)
  • This clustering of base pair substitutions is unusual and suggests that mutation may result from unique structural features of the PKD1 gene. (labome.org)
  • A typing assay based on a diagnostic mgpB gene PCR was developed, evaluated, and applied directly to urogenital specimens. (asm.org)
  • The PCR can be based on the MgPa-1/MgPa-3 primer set located in conserved regions of the mgpB gene and producing an amplified fragment of 281 bp, as previously described ( 14 , 15 ). (asm.org)
  • Methylation of the cytosine base in eukaryotic DNA (5mC) is an important epigenetic mark involved in gene silencing and genome stability. (sciencemag.org)
  • The few available non-cluster-based methods only assess broad differences in gene expression between lineages, hence failing to pinpoint the exact types of divergence. (biorxiv.org)
  • We introduce a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of (i) within-lineage differential expression by detecting associations between gene expression and pseudotime over an entire lineage or by comparing gene expression between points/regions within the lineage and (ii) between-lineage differential expression by comparing gene expression between lineages over the entire lineages or at specific points/regions. (biorxiv.org)
  • We analyze a 680 base pair fragment of the mitochondrial DNA cytochrome oxidase (COII) gene from 45 new (21 collection localities) and two previously recorded samples of Reticulitermes from California using parsimony and maximum likelihood methods. (usda.gov)
  • We present a phylogenetic hypothesis for 40 species in the bird family Paridae, based on comparisons of nucleotide sequences of the mitochondrial cytochrome- b gene. (bioone.org)
  • Given the complementary relationship between rRNA and the Shine-Dalgarno sequence in mRNA, it was proposed that the sequence at the 3'-end of the rRNA determines the capacity of the prokaryotic ribosome to translate a particular gene in an mRNA. (wikipedia.org)
  • Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. (nih.gov)
  • The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. (nih.gov)
  • Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. (nih.gov)
  • Increased discrimination at the strain level can be achieved by sequencing, analyzing and comparing highly variable loci (regions) in the organism's genome. (criver.com)
  • We focus on a novel assay utilizing this approach, called s elective 2′- h ydroxyl a cylation analyzed by p rimer e xtension sequencing (SHAPE-Seq), that can be used to characterize RNA secondary and tertiary structure. (pnas.org)
  • Here, we used a sequence-based genotyping approach to characterize worldwide plum germplasm including the potential progenitor Eurasian plum species. (nature.com)
  • This paper describes a new approach of generating suitable recommendations based on the active user's navigation stream. (inria.fr)
  • As disease detection technologies rapidly evolve, so too must the FDA's approach to reviewing these new innovations," said FDA Commissioner Scott Gottlieb, M.D. "The new policies issued today provide a modern and flexible framework to generate data needed to support the FDA's review of NGS-based tests, and give developers new tools to support the efficient development and validation of these technologies. (fda.gov)
  • In this new approach, the bases forming the backbone of the typical DNA molecule are viewed one by one in the act of replicating. (nanotech-now.com)
  • Starting with low-passaged, authenticated ATCC materials and using a standardized next-generation sequencing and hybrid assembly approach, ATCC produced complete reference-quality genomes by combining highly accurate short reads with the scaffolding ability of ultra-long reads. (atcc.org)
  • The approach has led to the definition of more than 73,000 fungal species hypotheses, which together rely on and combine more than half of the system's 817,130 public reference DNA sequences. (gbif.org)
  • Research is now underway to create a vision system for hardwood log inspection using a knowledge-based approach. (usda.gov)
  • To this end, we propose an alternative to the traditional subject domain specific design approach which is based on the use of competence description ontology and learner's competence records. (sciweavers.org)
  • Initial strategies for exome enrichment utilized a hybridization-based capture approach. (sigmaaldrich.com)
  • MRI of acute myocarditis: a comprehensive approach based on various imaging sequences. (biomedsearch.com)
  • A new approach of H.264/AVC deblocking filter based on motion activity in video sequences is proposed. (go.jp)
  • In this approach, a modified deblocking filter is used for low to moderate motion video sequences. (go.jp)
  • The use of logistic map to generate strong cryptographic sequences is novel in approach in terms of its use with a range of transmission techniques for wireless communication because it is easy to conceive and requires simple devices to generate the sequence. (igi-global.com)
  • The mature proteins were 94% identical to each other and 36% identical to the sequences of bacterial L-arginine:inosamine phosphate amidinotransferases. (labome.org)
  • Many studies have confirmed that base pairing between the Shine-Dalgarno sequence in mRNA and the 3' end of 16S rRNA is of prime importance for initiation of translation by bacterial ribosomes. (wikipedia.org)
  • MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Binomial hierarchical model and is capable of processing two billion reads in 24 CPU hours. (nih.gov)
  • Dash curves indicate inferred methylation ratio Beta distributions from low (Sample #1) or high sequencing depth (Sample #2). (nih.gov)
  • By combining name-based information from dozens of different authoritative sources like the Catalogue of Life , IRMNG and the World Register of Marine Species (affectionately known as 'WoRMS'), the backbone provides a consistent means of organizing all species-related content on GBIF.org-like datasets, occurrences and species pages-and enables all forms of taxonomic searching, browsing and reporting. (gbif.org)
  • Pyrosequencing is a highly flexible technology that lets you rapidly analyze short- to medium-length sequences fast and quantitatively with high accuracy. (qiagen.com)
  • A comparison between the sequencing results and bioinformatic sRNA predictions using Dynalign and RNAz revealed only a small overlap between the different approaches. (nih.gov)
  • A ) Expression of eight out of twelve new candidate sRNAs could be confirmed by northern blotting whereas the length of the probed RNA corresponded to the calculated length from the sequencing data. (nih.gov)
  • Sequencing of fragments produces data in the form of fragment counts ( X ). Similarly, a control experiment ( Right ) measures natural drop-off (fragments labeled Y ). The model parameters consist of the adduct probabilities (Θ), the Poisson rate for the number of adducts per molecule ( c ), and the drop-off probabilities in the control experiment (Γ). (pnas.org)
  • INSTALLATION See installation instructions: http://code.google.com/p/sequor/wiki/INSTALL USAGE With Sequor you can learn a model from sequences manually annotated with labels, and then apply this model to new data in order to add labels. (haskell.org)
  • In this thesis, we focus on the base-calling stage, during which base order is estimated from data collected through electrophoresis and florescence detection. (mit.edu)
  • As a first attempt to construct a phylogenetic framework for the genus, data from morphology and nuclear ITS sequences for 53 species and four outgroup taxa were analyzed. (bioone.org)
  • Its main advantages are: fast and selective data access plans, and intelligent combination of such plans, based on a summary of the document paths. (sciweavers.org)
  • Comparison of the sequence data with that of other known actin-capping and severing proteins shows no significant homologies, suggesting that Cap Z may be a member of a unique group of capping, nonsevering proteins. (labome.org)
  • Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). (harvard.edu)
  • Through our Enhanced Authentication Initiative, we have identified the key challenges with existing publicly available data and have developed a solution for improving the quality of reference genome sequences. (atcc.org)
  • This Ph.D. Dissertation inferred the historical processes that seem to have built the avian community assemblage restricted to the Amazonian floodplains based on their patterns of diversification and geological and climatic data. (usp.br)
  • We evaluate the method on simulated and real datasets from droplet-based and full-length protocols, and show that the flexible inference framework is capable of yielding biological insights through a clear interpretation of the data. (biorxiv.org)
  • the hybridization-based markers deployed in these studies have genetical and practical disadvantages, particularly in the context of applied agricultural research. (genetics.org)
  • Agilent offers other hybridization-based target enrichment technology options, also, for finding specific regions-of-interest. (agilent.com)
  • This came from their observation that the 3' terminal sequences of 18S rRNA from Drosophila melanogaster, Saccharomyces cerevisiae, and rabbit cells are identical: GAUCAUUA -3'OH. (wikipedia.org)
  • Results show that the use of exponential decay weighting schemes when taking into account non contiguous sequences to compute recommendations enhances the accuracy. (inria.fr)
  • If you're curious to see how P ROB C ONS performs on nucleotide sequence, try out P ROB C ONS RNA , an experimental version of P ROB C ONS with parameters estimated via unsupervised training on BRAliBASE II ! (stanford.edu)
  • The advent of DNA sequencing has revolutionized biological research by providing virtual blueprints of living organisms and offering insights into complicated biochemical processes. (mit.edu)
  • Each species hypothesis is assigned a DOI , establishing a stable, permanent reference for that particular hypothesis (sequences known to derive from organisms already in possession of formally described Linnaean scientific names can, of course, rely on those). (gbif.org)
  • However, it is now clear that inheritance not based on DNA sequence exists in multiple organisms, with examples found in microbes, plants, and invertebrate and vertebrate animals. (sciencemag.org)
  • Yet, it appears that biology is much richer: Many phenomena and mechanisms of nongenetic and/or non-DNA sequence-based inheritance have been described in a range of model organisms, challenging our perception of the well-established relationship between transmitted genotype and phenotype. (sciencemag.org)
  • Examples of non-DNA sequence-based inheritance and/or the inheritance of acquired traits have recently been reviewed elsewhere ( 7 - 11 ) and span many diverse organisms. (sciencemag.org)
  • HTG Edge system capabilities have been expanded to fully automate sample and targeted library preparation for next-generation sequencing. (cnbc.com)
  • CARLSBAD, Calif.--( BUSINESS WIRE )-- Thermo Fisher Scientific , the world leader in serving science, has entered into a long-term agreement with Novartis and Pfizer to develop and commercialize a multi-marker, universal next-generation sequencing (NGS) oncology test that will serve as a companion diagnostic (CDx) for non-small cell lung cancer (NSCLC) across multiple drug development programs. (businesswire.com)
  • Developments in next-generation sequencing (NGS) during the past decade have made it possible to economically sequence the mitochondrial and Y chromosomes in large number of individuals [ 12 ]. (nature.com)
  • A ) Length distribution of reads after 5′ end-linker and polyA-tail clipping of four sequenced C. trachomatis cDNA libraries generated from either total RNA or total RNA enriched for primary transcripts of reticulate bodies (RB) or elementary bodies (EB), respectively. (nih.gov)
  • Here we report the discovery, characteristics, development, and linkage mapping of 568 new barley SSRs from enriched small insert libraries and from new sequences in the public databases. (genetics.org)
  • Forty had the same sequence type in consecutive specimens. (asm.org)
  • Specimens collected from two men were repeatedly positive at intervals of 472 and 1,395 days, respectively, but the sequence types had changed. (asm.org)
  • Seventy-nine M. genitalium -positive specimens from 19 couples were investigated, and all partners initially had concordant sequence types, but one couple had discordant types at one time point before a newly introduced strain took over. (asm.org)
  • But without physical specimens or accepted scientific names, these sequences cannot not be linked to the Linnaean-based nomenclature Codes that set the rules governing the biological classification system. (gbif.org)
  • The detection can be performed by direct sequencing of the cDNA fragments using high-throughput sequencing technology ( 2 ). (pnas.org)
  • The identification of adduct formation can be performed by capillary electrophoresis (SHAPE-CE) or by high-throughput sequencing of cDNA fragments (SHAPE-Seq) ( 2 ) ( Fig. 1 ). (pnas.org)
  • For building the optimized test schedule, frequency based pseudo damage methodology called Relative Damage Spectrum (RDS) is incorporated.This method enhances the proving ground durability validation process by providing optimized test schedules to prevent redundant vehicle testing. (sae.org)
  • In hope of addressing this gap in scientific knowledge, experts from the University of Tartu Natural History Museum (home to the GBIF Estonia node) and the University of Gothenburg developed UNITE , a system that uses ribosomal DNA-based sequences to give an identity to these cryptic elements of fungal biodiversity. (gbif.org)
  • Using a method developed by Hunt, Shine and Dalgarno showed that the nucleotide tract at the 3' end of E. coli 16S ribosomal RNA (rRNA) is pyrimidine-rich and has the sequence -PyACCUCCUUA 3' OH. (wikipedia.org)
  • Sequencing provides a means of detecting the presence of fungal species in the absence of fruiting bodies. (gbif.org)
  • For sequences known only from environmental samples, this system has the advantage of giving unambiguous identities to species hypotheses. (gbif.org)
  • Base-calling on the major alone yields accuracy commensurate with single sequence approaches, and joint base-calling provides results for the minor which, while being of lesser quality, incurs no additional cost and can be ultimately used in the genome assembly process. (mit.edu)
  • Based on the Training Sequence (TS), this paper develops three Frequency Domain (FD) channel estimation approaches for diffuse wireless optical channels. (techrepublic.com)
  • Manassas, VA - October 1, 2019 - ATCC launched its new ATCC Genome Portal , a publicly available database of reference-quality genome sequences matched to authenticated ATCC biological materials that will help researchers interpret and reproduce their results with confidence. (atcc.org)
  • The work has now been published in Biomaterials Science ( http://pubs.rsc.org/en/content/articlelanding/2013/bm/c3bm60126a#!divAbstract ) and presentations on the work by first author, Giovanna Sicilia, have won First Prizes at the UK and Ireland Controlled Release Society and the Macro Group UK Young Researchers' Meeting. (nottingham.ac.uk)
  • InfoSci®-OnDemand Plus, a subscription-based service, provides researchers the ability to access full-text content from over 100,000 peer-reviewed book chapters and 26,000+ scholarly journal articles covering 11 core subjects. (igi-global.com)