• We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. (nih.gov)
  • In Georgia, clusters are inferred using a genetic distance threshold of 0.005 nucleotide substitutions per site among persons with HIV infection diagnosed during the most recent 3 years, with priority clusters defined as those that include four or more diagnoses during the most recent 12 months. (cdc.gov)
  • Cross-referencing with USGENE is possible, with direct links from the well-known genetic sequence database to corresponding PatBase Express records. (piug.org)
  • Collectively, these data extend our understanding of the genome characteristic of PCV4 as well as the molecular epidemiology and the genetic profile of PCV4 and PRRSV. (bvsalud.org)
  • To further understand the molecular epidemiology and genetic diversity of PEDV field strains, in this study the complete genomes of four PEDV variants (HN2021, CH-HNYY-2018, CH-SXWS-2018, and CH-HNKF-2016) obtained from immunized pig farms in central China between 2016 to 2021 were characterized and analyzed. (bvsalud.org)
  • This study lays the foundation for better understanding of the genetic evolution and molecular pathogenesis of PEDV. (bvsalud.org)
  • We employed nucleotide sequences of mitochondrial (ND6, ND6-ND3 intergenic spacer, ND3, ND2, COI, msh1 and 16S) and nuclear (28S and ITS2) genomic regions from several taxa to infer molecular phylogenetics and to examine the correspondence of morphological features with the underlying genetic information. (noaa.gov)
  • Genetic diversity has traditionally been accessed from pedigree, however, with the advances in molecular genetics new opportunities have emerged. (scirp.org)
  • Reciprocal monophyly evidenced through phylogenetic analyses, sequence divergence values for both molecular markers, and detailed morphological analyses, including scanning electron microscopy photomicrographs, revealed three new genetic lineages, i.e., species, as parasites of M. curema . (parasite-journal.org)
  • Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)
  • Genetic characterization of wild-type measles virus was analyzed using nucleotide sequencing from the C-terminal region from the N protein gene and phylogenetic analysis in 59 isolates from 16 provinces of China in 2004. (woofahs.com)
  • We completed this research to spell it out the measles genotype 858134-23-3 supplier circulating in China in 2004 also to Mouse monoclonal to IHOG supplement the data source of genetic features of China measles strains through the control stage of the condition. (woofahs.com)
  • Genetic relationships among the meningococcal carriage isolates were determined using core genome multilocus sequence typing analysis. (bmj.com)
  • Genetic distance analysis showed that the highest nucleotide differences was observed between S. maximus and S. rhombus species with a value of 0.09620 and, the lowest value (0.02482) was observed between S. maximus and S. maeoticus species. (dergipark.org.tr)
  • The genetic data was supported by the detected morphometric variations among the turbot species. (dergipark.org.tr)
  • Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. (lu.se)
  • Transposable elements (TEs) are mobile genetic sequences that comprise around 50% of our genomic DNA. (lu.se)
  • In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. (wikipedia.org)
  • This database is produced at National Center for Biotechnology Information (NCBI) as part of an international collaboration with the European Molecular Biology Laboratory (EMBL) Data Library from the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). (iospress.nl)
  • The rapidly growing number of genomic data has had a profound impact on how bioinformatics is being taught to biologists. (iospress.nl)
  • PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.For academic uses, PGEToolbox is available free of charge at http://bioinformatics.org/pgetoolbox/ . (stanford.edu)
  • The aim of the course is that the students acquire a general understanding of several major bioinformatics concepts and tools commonly used in biology and molecular biology and obtain training in designing and executing bioinformatics procedures aimed at answering scientific questions within various fields of biology. (lu.se)
  • The course gives an overview of the most commonly used applied bioinformatics methods within the fields of biology and molecular biology. (lu.se)
  • An accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. (omictools.com)
  • 2014) Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. (omictools.com)
  • Although it may seem that DNA sequence data is the answer to these problems there are still things that require morphological evidence, a practice that is as old as plant sciences itself. (nmmra.org)
  • Morphological data has been accumulating steadily for the past 250 years, but for the first 100 it mainly concerned the question of taxonomy. (nmmra.org)
  • There is a point where additional morphological characters add little extra value (due to specificity) and the important factor is the quality of the data rather than the quantity. (nmmra.org)
  • Phylogeny of Greya (Lepidoptera: Prodoxidae), based on nucleotide sequence variation in mitochondrial cytochrome oxidase I and II: congruence with morphological data. (dergipark.org.tr)
  • The pathogens isolated from plants were consistent with Fusarium solani as a result of morphological examination and molecular phylogenetic analysis. (online-rpd.org)
  • Molecular analysis was performed to support the morphological characteristics identified earlier. (online-rpd.org)
  • N. meningitidis isolates were evaluated for antibiotic susceptibility and characterised by whole genome sequencing. (bmj.com)
  • The project's goal was sequence and map all the genes in a human which required the capability to create and utilize a large sequence database. (wikipedia.org)
  • you will see in a live demonstration how to use the Entrez interface including filters, the advanced search page, and search strategies to collect and download a specific set of records, to narrow the search, and to use the precomputed relationships available in the Entrez system find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information. (piug.org)
  • In addition to the sequence databases, you will also learn how to access related information in HomoloGene, UniGene and Gene Expression Omnibus (GEO), how to use precomputed BLAST (BLink) to find homologous proteins and genes, and how to use the Graphical Sequence Viewer as a tool for exploring large and complex genomic sequences and their annotations. (piug.org)
  • Mycobacterial colonies were isolated from a popliteal lymph node aspirate sample and molecular typed by SNPs typing of the genes gyrB and rpsA , the 3′ region of the hsp65 gene and the internal transcribed spacer (ITS), and MIRU-VNTR analysis. (frontiersin.org)
  • SNP typing takes advantage of nucleotide changes in specific single-copy genes-i.e., gyrA, gyrB, groEL1, sodA, rpsA , and hsp65 -( 10 - 12 ) or chromosomal loci-i.e., 16S−23S rDNA internal transcribed spacer (ITS)-( 13 ) to use them as biomarkers for subspecies differentiation. (frontiersin.org)
  • Two nucleotides were different between the E. coli (Tn3) and H. ducreyi (pCb) genes that affected the amino-acid sequence. (lu.se)
  • BioSystems currently contains biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the EcoCyc ( Escherichia coli K-12 MG1655) subset of the BioCyc databases and is designed to accommodate other data in the future. (nih.gov)
  • Phylogenetic analysis of the order Pleuronectiformes (Teleostei) based on sequences of 12S and 16S mitochondrial genes. (dergipark.org.tr)
  • HIV molecular epidemiology research analyse viral gene sequences because of their availability but entire genome sequencing allows to make use of various other genes. (bioinf.org)
  • Within the last couple of years the raising option of HIV entire genome sequences provides permitted the evaluation of other hereditary regions which includes raised debate about whether full-length genome trees and shrubs should be utilized or which viral genes supply the greatest trees. (bioinf.org)
  • The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. (medscape.com)
  • DNA microarrays are simply platforms that consist of small solid supports onto which the sequences from thousands of different genes are attached at fixed locations. (medscape.com)
  • the resistance pattern to -lactams of these strains was determined by using the disc diffusion and E-test methods followed by molecular methods such as PCR of bla et bla genes. (who.int)
  • Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
  • Sequence variations in a number of genes for DNA repair in occupational toxicology for a more accurate risk and phase I/phase II metabolising enzymes have recently assessment of groups of workers. (cdc.gov)
  • 5 Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany. (nih.gov)
  • Genetics and Molecular Biology, 31, 284-292. (dergipark.org.tr)
  • PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. (stanford.edu)
  • Molecular 858134-23-3 supplier epidemiology of measles infections in China, 1995C2003 confirmed that genotype H1 was distributed through the entire nation which China includes a one broadly, endemic genotype. (woofahs.com)
  • Most research on HIV molecular epidemiology today use the part of the viral gene which has the protease (PR) and invert transcriptase (RT) coding locations. (bioinf.org)
  • The future of microbiological diagnostics and infection epidemiology is increasingly centred on rapid and point of care molecular testing, including the application of nucleotide sequencing technologies. (wellcomeconnectingscience.org)
  • This essay will outline the contributions made by DNA sequencing data to plant phylogeny and its limitations. (nmmra.org)
  • DNA sequencing provided a high resolution, reliable method for the construction of phylogeny. (nmmra.org)
  • Preliminary study on mitochondrial 16S rRNA gene sequences and phylogeny of flatfishes (Pleuronectiformes). (dergipark.org.tr)
  • Having less a known huge phylogeny prevents offering a definitive evaluation that would response this issue but simulated data offer an approximation which allows having both accurate tree and a recombination-free dataset. (bioinf.org)
  • A 27-taxon phylogeny of Plagiothecium based on nuclear ITS and plastid rpl16 intron DNA sequence data resolved Austrian and Chinese populations of P. handelii as sisters, in a clade with P. paleaceum, a julaceous Himalayan species with cochleariform leaves. (bioone.org)
  • One of the largest being GenBank which contains over 2 billion sequences. (wikipedia.org)
  • The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. (iospress.nl)
  • GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 115,000 distinct organisms. (iospress.nl)
  • GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. (iospress.nl)
  • Upon receipt of a sequence submission, the GenBank staff assigns an Accession number to the sequence and performs quality assurance checks. (iospress.nl)
  • The GenBank direct submissions group also processes complete microbial genome sequences. (iospress.nl)
  • Newly generated sequences were aligned with other sequences available in GenBank. (parasite-journal.org)
  • PCR items from the 59 viral isolates in the COOH-terminus from the nucleoprotein gene had 858134-23-3 supplier been available and sequenced. (woofahs.com)
  • Physique 2 phylogenetic tree of the N gene sequences of 59 wild-type measles isolates from China compared to the WHO reference sequences for each genotype. (woofahs.com)
  • The linear genome (14.7 kbp) of two isolates from Japanese and USA bell pepper cultivars were completely sequenced and compared. (microbiologyresearch.org)
  • Recently completed molecular studies of poliovirus isolates suggest that viral replication of vaccine-related polioviruses may have persisted for as long as 7 years in a patient with vaccine-associated paralytic poliomyelitis (VAPP) in whom common variable immunodeficiency syndrome (CVID) previously had been diagnosed. (cdc.gov)
  • In contrast, each subpopulation differed from wild type 1 poliovirus isolates by 19%-24% of VP1 nucleotides. (cdc.gov)
  • VP1 sequences of these isolates revealed a stepwise divergence from the Sabin 1 sequence at a rate of about 1.1% per year. (cdc.gov)
  • PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. (stanford.edu)
  • Here, we investigated two putative genotype 4/1 recombinants from southern Cameroon using a number of approaches, including standard Sanger sequencing, genotype-specific PCR amplification, and non-HCV-specific Illumina RNA sequencing (RNA-seq). (ox.ac.uk)
  • Previously known as the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Data Library (now known as European Nucleotide archive). (wikipedia.org)
  • 11 European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany. (nih.gov)
  • This can lead to a transitive annotation problem because there may be several such annotation transfers by sequence similarity between a particular database record and actual wet lab experimental information. (wikipedia.org)
  • Therefore, care must be taken when interpreting the annotation data from sequence databases. (wikipedia.org)
  • The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. (nih.gov)
  • Bayesian inference and maximum likelihood analyses were implemented using the data sets of LSU and cox1 independently. (parasite-journal.org)
  • L'inférence bayésienne et les analyses de vraisemblance maximale ont été mises en œuvre en utilisant les ensembles de données de LSU et cox1 indépendamment. (parasite-journal.org)
  • La monophylie réciproque mise en évidence par des analyses phylogénétiques, des valeurs de divergence de séquence pour les deux marqueurs moléculaires et des analyses morphologiques détaillées, y compris des photomicrographies au microscope électronique à balayage, a révélé trois nouvelles lignées génétiques, c'est-à-dire des espèces, qui sont parasites de M. curema . (parasite-journal.org)
  • However, few functions are freely available in Matlab to perform the sequence data analyses specifically required for molecular biology and evolution. (stanford.edu)
  • In conclusion: biochemical and molecular analyses of gene (s) responsible for aflatoxins synthesis is of great interest to assure food safety by detecting and preventing mycotoxin risk exposure. (cientperiodique.com)
  • Several downstream analyses are performed and their utility in applied ecology, evolutionary biology and molecular biology research will be discussed with guest lecturers. (lu.se)
  • After 4 weeks of conversion, we performed global analyses of RNA and protein levels by RNA-sequencing and mass spectrometry. (lu.se)
  • He won his second Nobel Prize for creating methods for sequencing nucleic acids, and his comparative approach is what sparked other protein biochemists to begin collecting amino acid sequences. (wikipedia.org)
  • Dayhoff and her team made use of their facilities for determining amino acid sequences of protein molecules in mainframe computers. (wikipedia.org)
  • Additionally, we estimated the evolutionary distances among these three species based on nucleotide and amino acid sequences of the mitochondrial CO1 gene. (pensoft.net)
  • Records in sequence databases are deposited from a wide range of sources, from individual researchers to large genome sequencing centers. (wikipedia.org)
  • Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. (iospress.nl)
  • Lots of groups other than the Roadmap screening centers have deposited such data. (cam.ac.uk)
  • a - d , f ) A simple way to gain insight into function is to use ribbon representation colored by sequence features: for example, domains ( a ), SNPs ( b ), exons ( c ), protein binding sites ( d ) and sequence conservation ( f ). ( e ) An effective way to show overall shape is with nonphotorealistic rendering using flat colors and outlines. (nature.com)
  • Today's tools are increasingly internet aware, often integrated tightly with structure databases ( Table 1 ), as well as with databases containing sequences and other features (for example, domains, single-nucleotide polymorphisms (SNPs), interactions). (nature.com)
  • We ing practice, different workload, and the use of personal are monitoring single nucleotide polymorphisms (SNPs) protection devices. (cdc.gov)
  • Some specimens were photographed and sequenced for two molecular markers, the large subunit (LSU) of nuclear rDNA and the cytochrome c oxidase subunit 1 ( cox1 ) of mitochondrial DNA. (parasite-journal.org)
  • Tanaka H, Dung LD, Higashi R, Tsukagoshi A (2016) A new interstitial ostracod species of the genus Paracobanocythere from Vietnam, with mitochondrial CO1 sequence data of three Asian species. (pensoft.net)
  • Here, we describe a new species from Vietnam and supply DNA sequence data of the mitochondrial cytochrome c oxidase subunit 1 ( CO1 ) gene from the three described Asian species. (pensoft.net)
  • The number of discovered sequences continued to grow allowing for a deeper comparative analysis of proteins than ever before. (wikipedia.org)
  • This led to many developments such as, probabilistic models of amino acid substitutions, sequence aligning and phylogenetic trees of evolutionary relationships of proteins. (wikipedia.org)
  • Molecular biologists view RNA structures and complexes with proteins to gain insight into RNA signal and message processing. (nature.com)
  • In the character-based approach, each position of an alignment represents a molecular character which may adopt different states in gene sequence data (e.g., nucleotides and deletions). (biomedcentral.com)
  • Genomics and proteomics have revolutionized biology but would not have been possible without developments in capillary sequencing, cDNA microarrays, and mass spectrometry, amongst other enabling technologies. (nih.gov)
  • There are, in conjunction with the genomics platforms built with SWEGENE support, in general systems for the immediate management of the large amounts of experimental data generated. (lu.se)
  • ClinVar provides standardized nomenclature for variants and phenotypes, a review status for variants, and links to related NCBI literature and molecular databases. (nih.gov)
  • 2013) Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. (omictools.com)
  • To test whether rare or subpolymorphic TGFBR1 variants were associated with CRC risk, we sequenced the gene's exons in a subset of patients. (ox.ac.uk)
  • F1 contains neutral training data, F2 contains pathogenic training data, F3 contains ASD variants. (lu.se)
  • 2020). Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. (lu.se)
  • As a result, the sequences themselves, and especially the biological annotations attached to these sequences, may vary in quality. (wikipedia.org)
  • This work demonstrates a useful general extension to dynamic alignment algorithms, as well as direct applications of that extension toward the development of molecular recorders, providing a necessary stepping stone for future biological work. (mit.edu)
  • BioSample contains descriptions of biological source materials used in studies that have data in other NCBI molecular databases such as Assembly, Nucleotide and SRA. (nih.gov)
  • BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. (dergipark.org.tr)
  • In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. (mdpi.com)
  • Throughout his career, his aim has been to combine experimental, theoretical and data analysis methods to obtain holistic understanding of biological and medical problems. (lu.se)
  • Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP (2017) Nucleotide-time alignment for molecular recorders, PLoS Computational Biology 13(5):e1005483. (mit.edu)
  • RT-PCR products from six patients who died from TBE between 2013 and 2017 were directly sequenced and analysed phylogenetically. (who.int)
  • Molecular Biology and Evolution, 11(1), 128-141. (dergipark.org.tr)
  • We have developed a Matlab toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. (stanford.edu)
  • He thanked CDC and KTL for their support in providing accurate genomic sequencing results of polioviruses in a timely manner, as this greatly facilitated planning and targeting the polio eradication activities. (who.int)
  • In 2021, molecular HIV analysis in Georgia identified clusters of rapid HIV transmission among Hispanic or Latino (Hispanic) gay, bisexual, and other men who have sex with men (MSM) in metropolitan Atlanta. (cdc.gov)
  • The clusters were detected through routine analysis of HIV-1 nucleotide sequence data obtained through public health surveillance ( 1 , 2 ). (cdc.gov)
  • In February 2021, GDPH identified three HIV clusters among Hispanic MSM using molecular analysis of HIV-1 nucleotide sequence data collected through routine surveillance ( 1 ). (cdc.gov)
  • The introduction of molecular analysis of the relationships between these major groups, in the form of DNA sequence data, has revolutionised the subject in the last twenty years. (nmmra.org)
  • Glaser J.I.**, Zamft B.M.*, Marblestone A.H.*, Moffitt J.R., Tyo K., Boyden E.S., Church G., Kording K.P. (2013) Statistical analysis of molecular signal recording, PLoS Computational Biology 9(7):e1003145. (mit.edu)
  • PIQMEE: Bayesian phylodynamic method for analysis of large datasets with duplicate sequences. (cdc.gov)
  • Several molecular typing methods have been developed to differentiate between M. avium subspecies and strains, such as single nucleotide polymorphism (SNP) typing and mini-satellite sequence analysis-mycobacterial interspersed repetitive-unit variable-number tandem repeats (MIRU-VNTR) ( 5 ). (frontiersin.org)
  • MIRU-VNTR analysis, on the other hand, uses mini-satellite sequences (tandem repeats of 10-100 nucleotides) dispersed at multiple loci in the bacterial genome. (frontiersin.org)
  • Multilocus sequence typing analysis identified 29 sequence types belonging to 12 clonal complexes. (bmj.com)
  • We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. (unito.it)
  • Genedata, a leading provider of advanced software solutions for drug discovery and life science research, today announced the release of Genedata Biologics™, a first-in-class, off-the-shelf software solution for comprehensive data management and analysis of biologics R&D activities. (genedata.com)
  • Genedata Biologics is the first, fully integrated data management and analysis platform for supporting the entire biologics R&D process. (genedata.com)
  • The practical part of the course provides laboratory and computer data analysis sessions that examine the application of molecular, specifically genomic, techniques to clinical practice. (wellcomeconnectingscience.org)
  • Data analysis, interpretation, display and dissemination. (wellcomeconnectingscience.org)
  • the analysis with CAOS [ 13 ] involves a complex workflow and was developed for classifying unidentified gene sequences. (biomedcentral.com)
  • The analysis is based on a novel representation of the gene sequence data, which enables a ranking of all alignment positions according to their diagnostic relevance, and subsequently their classification. (biomedcentral.com)
  • Because of the complexity of the data sets generated by microarray experiments, the use of data-analysis software is essential. (medscape.com)
  • Several commercial and public data-analysis tools have been developed for this purpose. (medscape.com)
  • The work presented in this thesis focuses on the bioinformatic methods for a TE-centric analysis of next- and third-generation sequencing technologies. (lu.se)
  • In this workshop you will explore the NCBI Entrez integrated biomedical literature and molecular database system and learn how to effectively use the Entrez system to find records of interest. (piug.org)
  • The second part of this workshop will concentrate on the use of NCBI's BLAST for sequence searching and some of the ancillary tools that are integrated with BLAST at NCBI but that no one usually sees. (piug.org)
  • We will examine how BLAST functions and what changes in the NCBI BLAST pages "below the fold" make a difference in the results of sequence searching. (piug.org)
  • Part of the NCBI data repositories. (snf.ch)
  • The Assembly resource provides access to genome assemblies for both submitted data and NCBI RefSeq assemblies. (nih.gov)
  • Assembly provides versioned accession identifiers for submitted and RefSeq assemblies, links to the components in the Nucleotide system and direct access to the downloads on the NCBI FTP site. (nih.gov)
  • BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases. (nih.gov)
  • Papadakis EN, Dokianakis DN, Spandidos DA: p53 codon 72 polymorphism as a risk factor in the development of breast cancer. (aktsignals.com)
  • As of 2013 it contained over 40 million sequences and is growing at an exponential rate. (wikipedia.org)
  • Release 142, produced in June 2004, contained over 40.3 billion nucleotide bases in more than 35.5 million sequences. (iospress.nl)
  • Our data strongly supported the monophyly of the genus Paragorgia, the family Coralliidae (precious corals), and a group of undescribed specimens resembling Sibogagorgia. (noaa.gov)
  • The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)
  • HIV molecular cluster detection can identify rapid HIV transmission among sexual networks involving ethnic and sexual minority groups, draw attention to the needs of affected populations, and advance health equity through tailored responses that address those needs. (cdc.gov)
  • This process is repeated to build specific oligonucleotide sequences. (medscape.com)
  • The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort. (biomedcentral.com)
  • For a standardized designation of the position of diagnostic molecular characters in taxon diagnoses, a reference sequence alignment and/or a reference sequence are recommended, facilitating comparability and reproducibility [ 1 ]. (biomedcentral.com)
  • Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)
  • Today's situation is very different: the rate at which structures are solved has greatly increased, with over 60,000 high-resolution protein structures now available in the consolidated Worldwide Protein Data Bank (wwPDB) 1 . (nature.com)
  • While retaining all capabilities of a forward simulation, SLiM utilizes sophisticated algorithms and optimized data structures that enable simulations on the scale of entire eukaryotic chromosomes in reasonably large populations. (stanford.edu)
  • Sequence profiling tools can find restriction enzyme sites, open reading frames in nucleotide sequences, and predict secondary structures. (showboat-alkmaar.nl)
  • Standard Reference Data cover a broad range scientific disciplines including atomic and molecular physics, chemical and crystal structures, fluids, material properties, biotechnology, optical character recognition and more. (showboat-alkmaar.nl)
  • Previous suggestions for applying divergence cut-off values of gene sequences to discriminate and define taxa (threshold-based approach), however, are based on the overall dissimilarity and are not character-based, i.e., do not use distinct molecular characters for separation and characterization [ 1 , 4 ]. (biomedcentral.com)
  • Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. (essex.ac.uk)
  • With the advent of molecular biology and the availability DNA sequencing techniques, using DNA sequences to infer evolutionary and taxonomic patterns started to take hold. (nmmra.org)
  • It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. (stanford.edu)
  • Many annotations of the sequences are based not on laboratory experiments, but on the results of sequence similarity searches for previously annotated sequences. (wikipedia.org)
  • 5 We used data of all cases that were confirmed at the National Reference Laboratory of NCZD by enzyme-linked immunosorbent assay (ELISA), immunofluorescence assay (IFA) and polymerase chain reaction (PCR). (who.int)
  • The list is based on the SNSF monitoring report on Open Research Data, which was published in February 2020 and in which the SNSF analysed the Data Management Plans (DMPs) of over 1,500 funded applications. (snf.ch)
  • We apply our technique to an in silico motor control neuroscience experiment, using the algorithm to estimate both timings of DNA-based data and the directional tuning of motor cortical cells during a center-out reaching task. (mit.edu)
  • Some aspects of structure visualization remain mostly the domain of the specialist, such as molecular motion and large-scale molecular assemblies. (nature.com)
  • Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168. (nih.gov)
  • However, in a few cases, molecular typing at subspecies level has been carried out and Mah has proved to be the most frequent isolate ( 6 , 7 , 9 ). (frontiersin.org)
  • Our aims were (1) to isolate and molecular type the causative agent, and (2) to determine antibiotic susceptibility in vitro so as to ensure the most appropriate antimicrobial therapy for the dog. (frontiersin.org)
  • Nucleotide sequences encoding the major capsid protein VP1 were determined for each isolate. (cdc.gov)
  • The first (day 11) isolate contained two subpopulations, equally divergent from the Sabin 1 vaccine strain (by 10% of VP1 nucleotides), and differing from each other by 6% of VP1 nucleotides. (cdc.gov)
  • These diseases are most a Gram stain was performed for the Lebanon, while the most recent Middle often caused by non-encapsulated strains suspect colony and the identification of East data concerning the prevalence were or non-typeable Haemophilus influenzae each isolate was completed using Rapid from 2007 [10]. (who.int)
  • Participants will generate their own data and analyse it on the course to make public health, clinical and infection control decisions. (wellcomeconnectingscience.org)
  • It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima's D test, Fu & Li's tests and Fay & Wu's H test. (stanford.edu)
  • In sequence identity the three terminals have a similar level of variation, suggesting that the geographic disjunction between the two populations of P. handelii is quite old. (bioone.org)
  • This document is an overview of the Entrez databases, with general information on searching and displaying data. (nih.gov)
  • Most importantly Entrez integrates data with links within and between databases. (nih.gov)
  • The Entrez system comprises 39 molecular and literature databases. (nih.gov)
  • As a result, despite our increased knowledge of the molecular bases of cancer, the translation to clinical medicine has lagged significantly behind. (nih.gov)
  • [ 7 ] They consist of a glass surface onto which oligonucleotides consisting of 25 bases are built a single nucleotide at a time. (medscape.com)
  • Once a sequence has been annotated based on similarity to others, and itself deposited in the database, it can also become the basis for future annotations. (wikipedia.org)
  • The need for sequence databases originated in 1950 when Fredrick Sanger reported the primary structure of insulin. (wikipedia.org)
  • Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing. (ox.ac.uk)
  • In addition, we found evidence to indicate that conformation as well as sequence was important for good hexon binding in our assays. (microbiologyresearch.org)
  • Molecular characters have been added in integrative taxonomic approaches in recent years. (biomedcentral.com)
  • You will also explore aspects of the literature databases (PubMed and PubMed Central) with emphasis on the linkages between the literature and molecular data. (piug.org)
  • Here we describe the isolation, molecular typing, and antibiotic susceptibility testing of the causative agent of a rare case of generalized mycobacteriosis in a crossbred dog. (frontiersin.org)
  • The UniProt database is an example of a protein sequence database. (wikipedia.org)
  • Searching in a sequence database involves looking for similarities between a genomic/protein sequence and a query string and, finding the sequence in the database that "best" matches the target sequence (based on criteria which vary depending on the search method). (wikipedia.org)