• Methods SARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. (medrxiv.org)
  • She explained that forming partnerships allows Spiral to focus on its "core competency" - developing upstream bioinformatics tools for things like sequence alignment and variant calling - and at the same time meet customers' requests for genomic data analysis tools that are tailored to their particular needs. (genomeweb.com)
  • Spiral's platform, Mangubat explained, handles the early stages of genomic data analysis, where "everybody has to do the exact same thing," including alignment, consensus calling, and variant detection. (genomeweb.com)
  • The agreement between Spiral and Omicia allows the companies to combine their respective products and offer informatics infrastructure that will provide capabilities for analyzing raw sequence data through to identifying clinically relevant genomic variants. (genomeweb.com)
  • The scientific entry was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes. (bcgsc.ca)
  • We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)
  • We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. (frontiersin.org)
  • Commenting on the research efforts of Dr. Stelly, Dr. Jonathan Wendel of Iowa State University lauded his history of accomplishments: "His training was in classical plant cytogenetics, but over the years he has expanded into many different aspects of plant genomics, including comparative mapping, the development of new tools for germplasm characterization, the creation and genomic evaluation of chromosome substitution lines, and genome sequencing. (cottoninc.com)
  • One article stated, "Genomic rearrangements caused by scattered homologous proviral sequences gave rise to countless genetic variations on which the evolutionary powers of selection and adaptation could work. (answersingenesis.org)
  • Leading the sequencing and analysis phases of the project, the Genomics Resource Center (GRC) at the Institute is a cutting-edge genomic sequencing and analysis center with a long history of high-quality microbial genomics research that has sequenced and analyzed more than 5,000 microbial genome sequences in just the past five years. (centerwatch.com)
  • Since the beginning of the modern genomic sequencing era, researchers have had to make a choice. (diwou.com)
  • Here, you'll find information on the use of nanopore sequencing for genomic epidemiology, including what to expect from the workflows available, how to choose a sequencing approach to suit your requirements, and what you'll need to get started. (nanoporetech.com)
  • Genomic epidemiology is the study of how variations in the genomes of pathogens, or their hosts, influence health and disease, including how common specific variations are, how they interact with environmental factors, and how they contribute to disease risk. (nanoporetech.com)
  • To find out more about the impact of genomic epidemiology via rapid pathogen genome sequencing, view the genomic epidemiology white paper. (nanoporetech.com)
  • We analyzed whole-genome sequencing data from 2,511 individuals in the Pan-Cancer Analysis of Whole Genomes (PCAWG) study as well as 489 individuals from four prospective cohorts and found distinct regional mutation type-specific frequencies in tissue and cell-free DNA from patients with cancer that were associated with replication timing and other chromatin features. (nature.com)
  • Oxford Nanopore have worked closely with the ARTIC Network , who have developed workflows for the rapid preparation and sequencing of SARS-CoV-2 whole genomes in use by scientists around the world. (nanoporetech.com)
  • Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States. (cdc.gov)
  • The amplicons were sequenced by next-generation sequencing using the Illumina MiSeq 150 paired end method. (scielo.br)
  • FINDINGS The next generation sequencing and phylogenetic analyses of the 11-segmented genome of the G10P[14] strain allowed classification as G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. (scielo.br)
  • Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. (warwick.ac.uk)
  • The amplicons were pooled by sample and then barcoded and sequenced using Next Generation Sequencing platforms. (cdc.gov)
  • In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. (niema.net)
  • Sequence alterations are abundant in cancer genomes but the proportion of fragments in cell-free DNA (cfDNA) that harbor tumor-specific (somatic) mutations is often low 8 , 9 , making it difficult to detect bona fide variants amidst background noise from sequence changes introduced in library construction and sequencing. (nature.com)
  • Here, we considered whether identifying somatic mutations genome-wide could enable the detection of an increased number of circulating tumor DNA (ctDNA) alterations and increase the detection of early stage disease. (nature.com)
  • Background Sequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. (medrxiv.org)
  • Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. (medrxiv.org)
  • Genomes are indicated by lines, and mutations are shown by different symbols. (virology.ws)
  • There are no mutations in the consensus sequence, even though every viral genome contains mutations. (virology.ws)
  • 1 Unlike HIV, these "ancient" retroviruses purportedly integrated themselves into the genome long ago and have since accumulated mutations that have rendered them unable to produce infectious, exogenous viruses. (answersingenesis.org)
  • The virus has been named Phoenix and was constructed through comparison of DNA sequences from the human endogenous retrovirus K family (HERV-K). 2 HERV-K is proposed to be a fairly young (less than 5 million years) family, as it still contains a complete set of genes (albeit with mutations) necessary for a retrovirus to produce infectious viruses. (answersingenesis.org)
  • 2 (HERVs throughout the genome have presumably accumulated different mutations, and through comparison a consensus sequence can be determined. (answersingenesis.org)
  • It is optimized for short reads such as that generated by Illumina and is capable of assembling large genomes such as the human genome. (wikipedia.org)
  • Service uses the Illumina COVIDSeq™ Next-Gen Sequencing workflow for accurate determination of the prevalence of new SARS-CoV-2 Variants (B.1.1.7 and others). (zymoresearch.com)
  • Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. (mdpi.com)
  • The genome sequencing will use two HTS platforms, Illumina and Pacific Biosciences, and multiple genome assembler software packages and assembly QA/QC pipelines to assemble and validate the resulting draft genome sequences. (centerwatch.com)
  • On the one hand there are highly accurate, short reads-the bread and butter sequences that comes from Illumina and Complete Genomics. (diwou.com)
  • This means that they end up with individual PacBio reads (these circular consensus, or CCS, reads) with roughly the same error rate as Illumina reads, but which are much longer than Illumina reads. (diwou.com)
  • Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1. (cdc.gov)
  • The diagram above shows a small subset of the viral genomes that are present in a virus stock. (virology.ws)
  • Until recently it was not possible to know the sequences of all the viral genomes present in a population such as that illustrated in the figure. (virology.ws)
  • Drug-Resistant Shigella flexneri 2a, California, USA, 2022 Find out how whole-genome sequencing helped guide treatment selection in this case of persistent shigellosis that was refractory to initial drug therapy. (medscape.com)
  • In this study, chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq) was performed to identify the AmtR regulon in C. glutamicum ATCC 14067. (frontiersin.org)
  • It claims that its platform can analyze a whole human genome from raw sequence data to a fully annotated list of genetic variants in about three hours. (genomeweb.com)
  • This COVID-19 sequencing service provides accurate surveillance efforts to detect and characterize emerging variants of SARS-CoV-2. (zymoresearch.com)
  • Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. (biomedcentral.com)
  • From initial characterisation of the SARS-CoV-2 virus genome to the rapid identification of variants, researchers are utilising nanopore sequencing to generate data essential to combating the spread of COVID-19. (nanoporetech.com)
  • F1 contains 401 de novo synonymous benign variants within the consensus coding sequence (CCDS) and identified from individuals not ascertained for any specific disorder. (lu.se)
  • Genomes of the detected pathogens were reconstructed and analyzed phylogenetically. (biomedcentral.com)
  • Researchers at the Institute for Genome Sciences at the University of Maryland School of Medicine have been awarded a research program contract from the FDA to sequence, assemble and annotate a population of bacterial pathogens using two high-throughput sequencing (HTS) technologies in support of the expansion of a vetted public reference database. (centerwatch.com)
  • We have worked with federal agencies and global scientific partners to sequence and analyze an extensive population of bacterial pathogens since our Institute launched in 2007 and are pleased to develop this reference database with the FDA. (centerwatch.com)
  • The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. (biomedcentral.com)
  • The unique features of nanopore technology have enabled its use by the scientific community for the rapid sequencing of pathogens in multiple outbreak situations, including Zika , Ebola , yellow fever , and swine flu . (nanoporetech.com)
  • SISPA is an effective method of analysing both the genome of a pathogen of interest (in the above example, a novel pathogen is identified) plus that of co-infecting pathogens in the same sample. (nanoporetech.com)
  • This infographic describes some of the approaches available for metagenomic and metatranscriptomic sequencing of SARS-CoV-2 samples. (nanoporetech.com)
  • However, storage of the raw sequence data can become prohibitively large, and computing consensus genome from sequence data can be slow and requires bioinformatics expertise. (niema.net)
  • SOAP (Short Oligonucleotide Analysis Package) is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. (wikipedia.org)
  • genomics genome sequencing genome assembly bioinformatics http://soap.genomics.org.cn http://soap.genomics.org.cn/soap1 http://bioinformatics.genomics.org.cn http://seqanswers.com/forums/showthread.php?t=43 Li, R. (wikipedia.org)
  • Bioinformatics software startup Spiral Genetics has raised $3 million in series A financing and signed a partnership with genome interpretation firm Omicia in a bid to reach customers in the clinical genomics analysis market. (genomeweb.com)
  • The GRC was formed to serve the global genomics and bioinformatics communities, and its reputation is built on both its deep history in sequencing, genomics and analysis, and its end-to-end service level from initial project consultation through publication. (centerwatch.com)
  • This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). (warwick.ac.uk)
  • Developing a comprehensive, curated database of microbial genome sequences and associated metadata will serve as a valuable reference to evaluate and assess HTS-based diagnostic devices. (centerwatch.com)
  • Our final dataset for phylogenetic and evolutionary dynamics analyses comprised 316 complete genomes including the 83 PR genomes obtained for this study and an additional 233 published genomes, mostly from the Americas. (cdc.gov)
  • analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)
  • Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses ( e.g. , homology-based prediction of structure or function). (biomedcentral.com)
  • One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). (warwick.ac.uk)
  • Modules provide IRMA with all the data and configuration necessary to assemble a particular virus genome. (cdc.gov)
  • Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. (biomedcentral.com)
  • From a dataset of 1 million trimmed mapped SARS-CoV-2 reads, it is able to compute the base counts and the consensus genome in 16 minutes, store the reads alongside the base counts and consensus in 50 MB, and optionally store just the base counts and consensus (without the reads) in 300 KB. (niema.net)
  • The resulting sequence reads were assembled into complete ZIKV genomes using the iVar ( 3 ) computational package designed for assemblies of amplicon-based sequencing. (cdc.gov)
  • The SOAP suite of tools can be used to perform the following genome assembly tasks: SOAPaligner (SOAP2) is specifically designed for fast alignment of short reads and performs favorably with respect to similar alignment tools such as Bowtie and MAQ. (wikipedia.org)
  • The sequence reads were analysed using CLC Genomics Workbench 6.0 and phylogenetic trees were constructed using PhyML version 3.0. (scielo.br)
  • Hence, assembly programs resort to de Bruijn graphs (dBG) of \(k\)-mers of short reads to compute a set of long contigs, each being a putative segment of the sequenced molecule. (lirmm.fr)
  • Other types of DNA sequence analysis, as well as preprocessing of the reads for assembly, use classical data structures to index all substrings of the reads. (lirmm.fr)
  • Shawn Baker, PhD, consultant at SanDiegOmics.com explains it like this… "if you have a 1% error rate and you sequence to 100X depth, at each base you'll get roughly 99 reads that look the same, say an "A", and one base that is different, say a "G". The consensus call would be to assume that the base is truly an "A" and ignore the "G" call. (diwou.com)
  • In this paper, PacBio showed that they can generate very high quality PacBio sequencing by reading the same molecule multiple times (~10 times on average) rather than comparing 10 separate reads together. (diwou.com)
  • The consensus sequences of the internal PCR primer hybridization sites were manually verified using reads from amplicons that spanned across the sites. (cdc.gov)
  • In an article appearing recently in the journal Science, a team of Los Alamos researchers -- in conjunction with researchers from Duke University, Harvard School of Public Health and the University of Alabama -- suggests using a consensus or genetic ancestor of the HIV-1 virus when developing vaccines, rather than basing vaccines on geographically specific strains of the virus. (sciencedaily.com)
  • By using two complementary sequencing platforms, GRC researchers will be able to cross-validate consensus sequences to generate the highest possible genome sequence accuracy. (centerwatch.com)
  • A human genome reference sequence is an accepted representation of the human genome sequence that is used by researchers as a standard for comparison to DNA sequences generated in their studies. (genome.gov)
  • Since then, researchers have worked to fill the gaps an improve the inaccuracies in the human genome sequence. (genome.gov)
  • Although previous studies on limited sets of RA-regulated genes have defined canonical RAREs as direct repeats of the consensus RGKTCA separated by 1, 2, or 5 nucleotides (DR1, DR2, DR5), we show that in mouse embryoid bodies or F9 embryonal carcinoma cells, RARs occupy a large repertoire of sites with DR0, DR8, and IR0 (inverted repeat 0) elements. (nih.gov)
  • Its pipeline includes the Variant Annotation, Analysis, and Selection tool, or VAAST, a tool that the company developed for functional interpretation of whole-genome sequence data that helps users identify candidate disease genes and causal alleles ( BI 7/1/2011 ). (genomeweb.com)
  • Curved links encode sequence similarity and outer data tracks represent consensus similarity statistics and orthologous genes. (bcgsc.ca)
  • Stanford law professor Hank Greeley asked the audience to consider a situation in which a doctor sequences a genome in order to find cardiac data, but also winds up finding genes for a very high cancer risk. (technewsworld.com)
  • Customers can either use a free version of the tool, which comes with limited functionality such as unlimited storage and an annotation pipeline, or they can purchase a more comprehensive "pro" version that includes access to VAAST, a tool for family tree-based analysis, and features for comparing multiple genomes and sharing analysis results. (genomeweb.com)
  • The GATB library (Genome Assembly & Analysis Tool Box https://gatb.inria.fr ) now includes an implementation of k-mer counting based on those ideas. (lirmm.fr)
  • Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E-SD-EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages. (iucr.org)
  • Starter pack and bundle options are available, providing everything you need to start sequencing, whether you're new to nanopore sequencing or getting started with SARS-CoV-2 analysis, at low cost per sample. (nanoporetech.com)
  • Quake announced last year that he sequenced his genome for US$48,000, and according to Altman's analysis, Quake's genome shows that Viagra is unlikely to work for him. (technewsworld.com)
  • Eleven markers located on chromosomes 1A, 2B, 5A, 5D, 7B, and 7D by the genome-wide association studies analysis showed significant associations with at least two resistance-associated traits in two of the environments. (unboundmedicine.com)
  • Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. (who.int)
  • Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) is a method that allows the study of protein complexes, in particular chromatin and transcription factor complexes, in a rapid and robust manner by mass spectrometry (MS). The method can be used in parallel with chromatin immunoprecipitation-sequencing (ChIP-seq) experiments to provide information on both the cistrome and interactome for a given protein. (nature.com)
  • All sequence data obtained for this study was submitted to GenBank: accession numbers MW122373-MW122455. (cdc.gov)
  • It is particularly suited to short read sequencing data. (wikipedia.org)
  • SOAPindel is a tool to find insertions and deletions from next generation paired-end sequencing data, providing a list of candidate indels with quality scores. (wikipedia.org)
  • The platform can be used for analyzing data from targeted, exome, and whole-genome sequencing projects. (genomeweb.com)
  • then only the maximum hit for all reference sequences will be grouped into primary data. (cdc.gov)
  • Instead it is an assembly of consensus sequences that are designed to deal with variation in the human population and uncertainty in the data. (scienceblogs.com)
  • This set of data, as intended, was a "reference" for the human genome, not representing one single person over the whole genome, but a collection of different - albeit anonymous - people. (genome.gov)
  • I am using samtools/bcftools to generate a 'de novo' consensus assembly for use with rc454 to clean my sequencing data. (biostars.org)
  • Making use of fast, streamlined library preparation methods, real-time nanopore sequencing and data streaming, and highly scalable nanopore sequencing technology, these workflows enable you to set up SARS-CoV-2 sequencing quickly and easily in your own lab. (nanoporetech.com)
  • According to companies like Complete Genomics , this is an exciting opportunity, because cost-effective sequencing means that it will be possible to collect very large data sets, which in turn can be used to understand the genetic basis of human disease. (technewsworld.com)
  • Data from COVID-19 case investigations, contact tracing, the Commonwealth's immunization registry and whole genome sequencing were collated and analysed as part of this study. (who.int)
  • The ongoing Human Genome Project, which aims to have a working draft of our entire genetic blueprint by February next year, will produce a "consensus" sequence for the typical human. (newscientist.com)
  • During the Fifty-ninth Session of the World Health Assembly in May 2006, a working group tried to reach a consensus on the draft resolution by the intergovernmental meeting called for that purpose on 5 April 2006. (who.int)
  • Four genomes - The illustration, originally part of a poster , shows syntenic relationships between human, chimpanzee, mouse and zebrafish genomes. (bcgsc.ca)
  • A few weeks back, we published a review about the development and role of the human reference genome. (scienceblogs.com)
  • This week, 10 major drugs companies and the Wellcome Trust, the world's largest medical charity, are unveiling a plan to map the variability of the human genome within two years. (newscientist.com)
  • Many families of endogenous retroviruses exist throughout the human genome (forming as much as 8% of the genome), as well as throughout the genomes of most other living organisms. (answersingenesis.org)
  • Scientists, in a recent Genome Research article, 2 claim to have reconstructed an infectious retrovirus that purportedly incorporated itself into the human genome less than 5 million years ago. (answersingenesis.org)
  • 1 , 2 The scientists involved in this recent study compared sequences of HERVs from many parts of the human genome and constructed a retroviral sequence they believe resembles the sequence of the "ancestral" retrovirus of this family. (answersingenesis.org)
  • 2 ) A virus containing the ancestral sequence was produced and found capable of infecting a human cell line. (answersingenesis.org)
  • Abstract: Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. (lirmm.fr)
  • In the human genome, more than 360000 potentially G4-forming sequences can be found. (brc.hu)
  • The scientists responsible for assembling and updating such reference sequences aim to provide the highest-quality, best possible consensus representations of the sequence and structural diversity found in the human genome among populations. (genome.gov)
  • At the completion of the Human Genome Project back in 2003, scientists achieved a major milestone - a DNA sequence that covered 99 percent of the human genome's gene-containing regions and was of 99.99 percent accurate. (genome.gov)
  • It was an example of a human genome off which scientists could base research studies or compare other human genomes. (genome.gov)
  • The Human Genome Reference Sequence is not an example of one human but represents many different varieties of human genomes. (genome.gov)
  • The work is published in the paper entitled, " Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome " published in Nature Biotechnology . (diwou.com)
  • The consensus coding sequences of human breast and colorectal cancers. (ncbcs.org)
  • The elucidation of the human genome sequence has made it potential to ascertain genetic alterations in cancers in unprecedented component. (ncbcs.org)
  • Results: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. (warwick.ac.uk)
  • They have also worked tremendously hard to represent places in the genome where humans are different. (genome.gov)
  • Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. (warwick.ac.uk)
  • Abstract: New technologies have tremendously increased sequencing throughput compared to traditional techniques, thereby complicating DNA assembly. (lirmm.fr)
  • It was argued that the sequence information currently available was insufficient to provide consensus information across the full range of virus strains available. (who.int)
  • The Committee concluded that full-length genome sequences from additional variola major and minor strains, particularly Congo 70 and Somalia 77, should be determined and that additional clone libraries from selected strains should be prepared. (who.int)
  • and in sequencing of entire genomes of viruses from numerous different strains. (who.int)
  • The genome sequence was generated using overlapping PCR amplicons spanning the genome. (cdc.gov)
  • claiming that two homologous chromosomes paired between complementary sequences lead to the formation of a cross-stranded structure that physically links the two component helices. (iucr.org)
  • Suppose you want to string together the consensus sequences from all the contigs in an assembly, or chromosomes in a genome, or exons in a gene, etc. (dnastar.com)
  • Five quantitative trait loci (QTLs) on chromosomes 1A, 2B, 7B, and 7D overlapped or were in close proximity to previously reported QTLs based on the consensus and physical maps using the reference sequence of bread wheat (IWGSC RefSeq v1.0). (unboundmedicine.com)
  • The Assembly requested the Director-General to appoint a new group of experts to establish what research, if any, must be carried out in order to obtain consensus on the timing for the destruction of the existing variola virus stocks. (who.int)
  • 1999), attended also by 10 advisers representing fundamental and applied research and regulatory agencies, the Committee first focused on the need for further research on the variola virus in order to obtain consensus on the date of destruction of virus stocks. (who.int)
  • 8. The Secretariat acknowledges that there is no consensus among Member States on a proposed new date for the destruction of variola virus stocks. (who.int)
  • MAIN CONCLUSIONS The genetic characterisation of the G10P[14] strain from Honduras suggests that its genome resulted from multiple reassortment events which were possibly mediated through interspecies transmissions. (scielo.br)
  • Copies are 91% identical to the consensus. (girinst.org)
  • Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. (eur.nl)
  • The outputted consensus sequence is identical to the reference (see the BLAST alignment graphic at the bottom of the post) till it is truncated at ~5000 of ~7000 bp. (biostars.org)
  • Virologists now understand that virus populations are not made of a single member with a defined nucleic acid sequence. (virology.ws)
  • To address these challenges, we developed an approach, called GEnome-wide Mutational Incidence for Non-Invasive detection of cancer (GEMINI), that can identify a much larger number of somatic alterations in cfDNA (Fig. 1 ). (nature.com)
  • The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK. (biomedcentral.com)
  • We show that multiple variations of their canonical fold can be used to adapt to different single-stranded sequences with a large range of affinities. (nih.gov)
  • METHODS For the sample detected as G10P[14], 10% suspension was prepared and used for RNA extraction and sequence independent amplification. (scielo.br)
  • Preparation of clinical research samples via SISPA (Sequence-Independent, Single Primer Amplification), followed by nanopore sequencing, is an effective method of rapidly identifying unknown and novel infectious agents and generating consensus sequences. (nanoporetech.com)
  • All multiple sequence alignments were screened for recombination breakpoints using Recombination Detection Program (RDP4) ( 5 ) and no evidence of recombination was found. (cdc.gov)
  • This approach lays the groundwork for non-invasive cancer detection using genome-wide mutation features that may facilitate cancer screening and monitoring. (nature.com)
  • A total of 91 samples were sequenced but only 83 genomes assembled with more than 75% coding sequence coverage at 10X depth. (cdc.gov)
  • Scientists around the world are using nanopore sequencing to rapidly sequence and analyse SARS-CoV-2 virus genomes. (nanoporetech.com)
  • Visit the Resource Centre to view the latest publications, presentations, and more from scientists using nanopore sequencing to research COVID-19. (nanoporetech.com)
  • Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. (nih.gov)
  • Each was jointly instrumental in leading this cotton genome sequence assembly project which involved 54 individuals at 11 institutions on 3 continents. (cottoninc.com)
  • Genome Research. (wikipedia.org)
  • At the time, front page exposure of this sort has made Circos a very popular tool for visualization in genomics, and in particular, in cancer research where there is a need to illustrate differences between genomes. (bcgsc.ca)
  • These community building efforts include research projects in chromosome substitution lines, SNP markers, and genome sequencing to name a few. (cottoninc.com)
  • Commenting on the research efforts of Drs. Zhang and Chen, Dr. David Stelly of Texas A&M University lauded their accomplishment: "It is remarkable because of the complexity of the cotton genome, which is not only tetraploid, but riddled with extensive sequence redundancies from repetitive elements and residual duplications from multiple levels of paleopolyploidy. (cottoninc.com)
  • The Los Alamos research team recommended using a consensus sequence obtained from the Subtype C of the HIV-1 virus as a basis for vaccines in regions where the C subtype is most prevalent. (sciencedaily.com)
  • Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. (warwick.ac.uk)
  • The development of deep sequencing methods such as 454 pyrosequencing has now made it possible to study the quasispecies. (virology.ws)
  • All multiple sequence alignments were generated with MAFFT ( 4 ) with subsequent manual editing. (cdc.gov)