• The platform can be used for analyzing data from targeted, exome, and whole-genome sequencing projects. (genomeweb.com)
  • By combining whole exome sequencing, machine learning, and network analysis, researchers have identified new, ultra-rare gene mutations within specific biological pathways that may contribute to eating disorders. (news-medical.net)
  • Background De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. (bmj.com)
  • Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. (bmj.com)
  • Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. (cdc.gov)
  • Diagnostic Yield and Treatment Impact of Targeted Exome Sequencing in Early-Onset Epilepsy. (cdc.gov)
  • A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several times in the genome and is thought to play the same role in its different locations. (wikipedia.org)
  • Therefore, to capture the heterogeneity of the HEV quasispecies, including recombination events and SNP that occur with very low frequencies, we developed new sequencing approaches for HEV genotype 3 based on the amplification of the near full-length genome of HEV by long-range PCR (lrPCR) followed by subsequent next-generation sequencing (NGS) and third-generation sequencing. (nature.com)
  • The consensus sequence was reconstructed from the Ensembl genome annotation. (girinst.org)
  • The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. (girinst.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)
  • 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)
  • The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
  • Plurality consensus sequences are returned in the main folder and are named after the virus genome or gene segment class label, see the IRMA output page for more details . (cdc.gov)
  • Genome Sequencing in the Clinic – The question is not whether the glass is half-full or half-empty but whether or not the glass is the right tool. (cdc.gov)
  • This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. (nih.gov)
  • Here we have examined LANA interactions with host chromatin on a genome-wide scale using ChIP-seq, and show that LANA predominantly targets human genes near their transcriptional start sites (TSSs). (nih.gov)
  • 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)
  • To find out more about the impact of genomic epidemiology via rapid pathogen genome sequencing, view the genomic epidemiology white paper. (nanoporetech.com)
  • Why nanopore for SARS-CoV-2 whole-genome sequencing? (nanoporetech.com)
  • See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
  • RAPIDOMICS: rapid genome-wide sequencing in a neonatal intensive care unit-successes and challenges. (cdc.gov)
  • 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)
  • Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
  • 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)
  • Conclusions The present work defines at the genomic-wide level the kinetics of binding of Crz1 to gene promoters in response to alkaline stress, confirms diverse previously known Crz1 targets and identifies many putative novel ones. (figshare.com)
  • We've had targeted capture on the brain lately as we work with collaborators to put the finishing touches on our HLS-CATCH method for selecting large genomic elements using Cas9 guides and the SageHLS system. (sagescience.com)
  • Feasibility of genomic profiling with next-generation sequencing using specimens obtained by image-guided percutaneous needle biopsy. (cdc.gov)
  • The Parkinson's disease genes pink1 and parkin , which encode a mitochondrially targeted protein kinase, and an E3 ubiquitin ligase, respectively, participate in a key mitochondrial quality-control pathway that eliminates damaged mitochondria. (sdbonline.org)
  • Free NFKB dimers translocate to the nucleus, bind to the kappa B element of gene promoters and induce or repress the transcription of target genes. (frontiersin.org)
  • a regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. (insdc.org)
  • Here, we present evidence that the promoter regions of intellectual disability-associated genes are uniquely enriched in LTR sequences of the MER41 HERVs. (biorxiv.org)
  • Of note, functionally-relevant differences between humans and chimpanzees are observed regarding the 3 main components of this pathway: i) the protein sequences of immunes TFs binding MER41 LTRs, ii) the insertion sites of MER41 LTRs in the promoter regions of ID-associated genes and iii) the protein sequences of the targeted ID-associated genes. (biorxiv.org)
  • Gene Ontology analysis confirmed the relevant impact of calcineurin/Crz1 on a set of genes involved in glucose utilization, and uncovered novel targets, such as genes responsible for trehalose metabolism. (figshare.com)
  • This approach provides a means to gain access to novel genes expressed in various cell types by partitioning mRNAs containing common sequence elements using RNA-binding proteins. (duke.edu)
  • Regions of the L. killicki ( L. tropica ) and L. major genes sequences were scanned using BLAST program and subsequently compared using appropriate bioinformatic tools Chromas and MEGA. (who.int)
  • On the contrary, mutations that destroy conserved nucleotides in the consensus sequence are known as down mutations. (wikipedia.org)
  • These types of mutations down-regulate transcription since RNA polymerase can no longer bind as tightly to the core promoter sequence. (wikipedia.org)
  • Missense mutations altering a consensus PPPXY sequence of the alpha, beta or gamma subunits reproduced the increase in channel activity found in mutants in which the entire cytoplasmic C-termini are deleted. (nih.gov)
  • Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. (nature.com)
  • A study of nearly 6,000 families, combining three genetic sequencing technologies, finds that mutations that occur after conception play an important role in autism. (news-medical.net)
  • for example, kinases such as MAP kinases, JAK, PI3K and many others, when activated upon a specific stimulus in a specific cellular context, will not phosphorylate one target only, but usually a subset of different protein targets which will collectively lead to the expected stimulation. (eurogentec.com)
  • To determine if the anti-PTM antibody does recognize the protein member in a specific assay, it is advised to perform a western blotting experiment, and refer to the size of the target protein member to assess its phosphorylation state. (eurogentec.com)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • One of the most important functions of the tumor suppressor p53 protein is its sequence-specific binding to DNA. (nih.gov)
  • Our results are consistent with a model of the p53-DNA interactions involving one-dimensional migration of the p53 protein along the DNA for distances of about 1000 bp while searching for its target sites. (nih.gov)
  • Finally, splice sites (sequences immediately surrounding the exon-intron boundaries) can also be considered as consensus sequences. (wikipedia.org)
  • The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. (rcsb.org)
  • This machinery recognizes pre-mRNA sequences at several motifs - the 5′ and 3′ splice sites, the branch point, and polypyrimidine tracts - positioned at exon-intron boundaries [ 4 ]. (biomedcentral.com)
  • In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. (wikipedia.org)
  • This is a graphical representation of the consensus sequence, in which the size of a symbol is related to the frequency that a given nucleotide (or amino acid) occurs at a certain position. (wikipedia.org)
  • Each kinase will phosphorylate its substrates on amino acid patterns sharing sequence similarities, and many publications describe the consensus sequences recognized by particular kinases. (eurogentec.com)
  • HiFi reads generated with CCS are aligned to a reference sequence, amino acid changes are identified using statistical test. (pacb.com)
  • Position-specific scoring matrix Regular expression - denoting multiple sequences of symbols in formal language theory Sequence motif Sequence logo Pierce, Benjamin A. 2002. (wikipedia.org)
  • This proline-rich sequence, referred to as the PY motif, is known to be a site of binding by proteins bearing a WW domain. (nih.gov)
  • These host LANA-binding sites are generally found within transcriptionally active promoters and display striking overrepresentation of a consensus DNA sequence virtually identical to the LBS1 motif in KSHV DNA. (nih.gov)
  • A personal cancer treatment vaccine that targets distinctive "neoantigens" on tumor cells has been shown to stimulate a potent, safe, and highly specific immune anti-tumor response in melanoma patients, report scientists from Dana-Farber Cancer Institute and the Broad Institute of MIT and Harvard. (news-medical.net)
  • Monitoring of cancer patients via next-generation sequencing of patient-derived circulating tumor cells and tumor DNA. (cdc.gov)
  • A new preprint has landed on BioRxiv that reports on high-accuracy circular consensus sequencing (CCS) on the PacBio Sequel. (sagescience.com)
  • To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. (nature.com)
  • Scientists around the world are using nanopore sequencing to rapidly sequence and analyse SARS-CoV-2 virus genomes. (nanoporetech.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)
  • Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
  • It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. (wikipedia.org)
  • Specific sequence motifs can function as regulatory sequences controlling biosynthesis, or as signal sequences that direct a molecule to a specific site within the cell or regulate its maturation. (wikipedia.org)
  • The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are variable. (wikipedia.org)
  • N-glycosylation is well known to occur at asparagine residues in the canonical consensus sequence N-X-S/T, but has also been identified at a small number of N-X-C motifs including the Asn491 residue of human serotransferrin. (nist.gov)
  • Here we report additional novel glycosylation sites within non-canonical consensus motifs, in the conformation N-X-C, based on mass spectrometry analysis of partially-deglycosylated glycopeptide targets. (nist.gov)
  • Spiral markets cloud- and cluster-based software for sequence alignment, consensus calling, and variant calling, filtering, and annotation. (genomeweb.com)
  • Optionally, if an HMM profile is provided in your module, one can use it to globally align the plurality consensus to the profile and also create an amended alignment. (cdc.gov)
  • will appear in main folder for the plurality alignment and also in the amended_consensus folder. (cdc.gov)
  • versus the amended consensus alignment. (cdc.gov)
  • First of all we proceeded to an alignment using the CLUSTAL W program to each Leishmania species and for the selected gene (cysteine protase b) (the alignment use published sequences and sequences which were sequenced in our laboratory). (who.int)
  • The plurality consensus sequence is very useful when used with the BAM file to look at minor variants, since the most frequent allele will appear in the reference. (cdc.gov)
  • The second type of base amendment is for consensus allele quality control . (cdc.gov)
  • IRMA uses both the average consensus allele quality score as well as the consensus allele coverage depth. (cdc.gov)
  • HiFi reads from sequenced amplicons are separated by locus and allele using customized "guide" sequences supplied by the user. (pacb.com)
  • Consensus sequences that pass quality filters can be used with downstream workflows such as mapping, variant calling, and allele assignment. (pacb.com)
  • a model has been proposed, where 14-3-3 binding to H3S10ph at target promoters is stabilized by additional acetylation of H3K9 or H3K14. (eurogentec.com)
  • a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (insdc.org)
  • Further analysis of the binding sites allowed refining the consensus sequence for Crz1 binding to gene promoters and the effect of chromatin accessibility in the timing of Crz1 recruitment to promoters. (figshare.com)
  • Single Molecule, Real-Time (SMRT) sequencing enables you to detect all variant types such as structural variants, rare SNPs, indels, copy number variation, microsatellites, haplotypes, and phased alleles while sequencing through low complexity regions like repeat expansions, promoters, and flanking regions of transposable elements. (pacb.com)
  • Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as an up mutation. (wikipedia.org)
  • 2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription. (insdc.org)
  • Glucose and GLP-1 also synergistically activated NFAT (nuclear factor of activated T-cells)-mediated transcription from a minimal promoter construct containing tandem NFAT consensus sequences. (diabetesjournals.org)
  • Population-based Sanger sequencing has been shown to miss minor variants with a frequency below 20% 20 . (nature.com)
  • In November 2019, China and France jointly issued the Beijing Call for Biodiversity Conservation and Climate Change , calling for the world to "define and adopt an ambitious and realistic post-2020 global biodiversity framework building on the Aichi Biodiversity Targets and the lessons learned from the implementation of the Strategic Plan for Biodiversity 2011-2020. (lu.se)
  • This has been recognized in various national and international resolutions and declarations, including SDG targets 3.81 and 16.72 (September 2015), the Political Declaration of the High-Level Meeting on Universal Health Coverage3 (September 2019) and the Astana Declaration on Primary Health Care4 (October 2019). (who.int)
  • Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. (frontiersin.org)
  • Last week, Oxford Nanopore announced the PromethION 2 ("P2") Solo sequencer and a new collaboration with 10X Genomics to enable a streamlined workflow for sequencing full-length transcripts in single reads. (bio-itworld.com)
  • Oxford Nanopore Technologies provides the fastest SARS-CoV-2 sequencing, at low cost, and high quality. (nanoporetech.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)
  • This experience has supported the rapid deployment of nanopore sequencing in the COVID-19 pandemic. (nanoporetech.com)
  • Their foundational work, and that of Nikki Freed and Olin Silander , form the core of the workflows available for the nanopore sequencing of SARS-CoV-2. (nanoporetech.com)
  • 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)
  • 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)
  • Visit the Resource Centre to view the latest publications, presentations, and more from scientists using nanopore sequencing to research COVID-19. (nanoporetech.com)
  • 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)
  • Both proteins consist of three domains: two FKBP12-like domains termed FK1 and FK2 and a tetratricopeptide repeat domain that targets binding to Hsp90. (unboundmedicine.com)
  • This example identified consensus for proteins encoded by first and second in-frame downstream AUG. The total information contents were 8.8 and 7.0 bits for these sites, respectively. (biomedcentral.com)
  • As a means to identify cellular RNA targets for these proteins, we devised combinatorial shape libraries representing naturally derived 3' untranslated regions and were able to select a structurally related subset of transcripts that bound to Hel-N1. (duke.edu)
  • She said that Spiral has some undisclosed customers who are involved in early-stage clinical diagnostic development and agri-genomics and it has begun exploring opportunities in pharma where companies are just now starting to use sequencing to develop better drugs. (genomeweb.com)
  • allow proceeding to the in silico comparative genomics analysis of Leishmania DNAs and annotating the sequences identified. (who.int)
  • Other parameters are available to restrict the quality of the consensus alleles as part of the amended consensus. (cdc.gov)
  • The coverage table will also be amended when consensus alleles fail to pass thresholds. (cdc.gov)
  • It has also been demonstrated that STAT1 (Signal Transducer And Activator Of Transcription 1), a transcription factor (TF) crucially involved in the IFNγ pathway, binds consensus sequences that, in humans, are located with a high frequency in the LTRs (Long Terminal Repeats) of the MER41 family of primate-specific HERVs (Human Endogenous Retrovirus). (biorxiv.org)
  • Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. (frontiersin.org)
  • This infographic describes some of the approaches available for metagenomic and metatranscriptomic sequencing of SARS-CoV-2 samples. (nanoporetech.com)
  • Two approaches were developed to identify unique sequences to L. major in the first case and to L. tropica in the second. (who.int)
  • This report documents the progress made in achieving the targets and milestones of the Polio Eradication and Endgame Strategic Plan 2013-2018 and proposes the steps to be taken to interrupt the transmission of wild poliovirus and achieve other milestones of the Polio Eradication and Endgame Strategic Plan 2013-2018. (who.int)
  • Explore the targeted sequencing applications and workflows . (pacb.com)
  • Click "Sequence Details" to view all sequence information for this locus, including that for other strains. (yeastgenome.org)
  • Direct evidence linking the INK4A locus to tumorigenesis was provided by the targeted disruption of exon 2 of INK4A in mice. (medscape.com)
  • Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. (frontiersin.org)
  • Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations. (frontiersin.org)
  • providing sequencing data suitable to addressing challenging and outstanding problems in plant systematics. (frontiersin.org)
  • Together, these data provide a mechanistic basis for considering pinealocytes a target of TNF and reinforce the idea that the suppression of pineal melatonin is one of the mechanisms involved in mounting an innate immune response. (frontiersin.org)
  • Our analysis partners offer several solutions for analysis of targeted sequencing data. (pacb.com)
  • The study gathered preoperative imaging data (MRI, ultrasound, and molybdenum target examination) and intraoperative and postoperative pathological information. (bvsalud.org)
  • The sequences were analyzed in silico by BLAST searching for homologies with other DNAs deposited in the local and public data bases. (who.int)
  • For example, developed and developing nations disagree on whether derivatives of genetic resources (such as genetic sequencing data) should be shared. (lu.se)
  • As of the end of June 2014, two countries in the Region, Cameroon and Equatorial Guinea, have been confirmed, based on available genetic sequencing data, as polio-exporting countries. (who.int)
  • Accordingly, the present invention envisions an isolated nucleic acid encoding the GEF-H1S polypeptide of SEQ ID NO:2, as well as an isolated nucleic acid comprising the sequence of SEQ ID NO:1. (justia.com)
  • Using a competition assay on agarose gels we found that the p53 consensus sequences in longer DNA fragments are better targets than the same sequences in shorter DNAs. (nih.gov)
  • The sequences identified in the previous section of the work were used to design a combinations of 6 primers in 8 distinct regions of the target sequences for the amplification of a selection of reference DNAs belonging to the different Old World Leishmania species. (who.int)
  • 99% single-molecule read accuracy) to sequence targets ranging in size from several hundred base pairs to 20 kb. (pacb.com)
  • CCS generates a highly accurate reads based on building consensus from the multiple passes of forward and reverse strands of the insert DNA incorporated into a SMRTbell molecule. (pacb.com)
  • Thus a consensus sequence is a model for a putative DNA binding site: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized sequence that represents the predominant base at each position. (wikipedia.org)
  • In the present study, we demonstrate that IRE1α (also known as ERN1) and its downstream target, XBP1, are activated in skeletal muscle of mice upon injury. (elifesciences.org)
  • Such information is important when considering sequence-dependent enzymes such as RNA polymerase. (wikipedia.org)
  • We opted for conserved sequences between species, presenting enough sequence heterogeneities to be considered for the design of species- specific LAMP primers: such primers would allow the selective amplification of the DNA targets. (who.int)
  • According to a procedure that has been previously validated for the identification of species - specific targets among which some fragments would fit into the second category of sequences expected. (who.int)
  • It is likely to identify unique sequences to L. major of this type. (who.int)
  • The Advanced Molecular Detection (program established the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) to coordinate SARS-CoV-2 sequencing. (cdc.gov)
  • Since the regulatory function of these sequences is important, they are thought to be conserved across long periods of evolution. (wikipedia.org)
  • The coordinate space is usually shared with the reference seeds in the consensus folder of the module. (cdc.gov)
  • We demonstrate that the distinct FK linker sequences per se do not account for lack of potentiation activity by FKBP51. (unboundmedicine.com)
  • The amount of information gathered via next-generation sequencing has made the diagnosis of genetic disorders quicker and more accessible to clinicians than ever before, but with expanded testing options come questions about ordering the correct type of testing. (news-medical.net)
  • Implementation of cancer next-generation sequencing testing in a community hospital. (cdc.gov)
  • Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. (frontiersin.org)
  • In case of homologies identified with the other Leishmania species, these sequences were compared to L. major and/or L. tropica using MEGA software. (who.int)
  • Transposons act in much the same manner in their identification of target sequences for transposition. (wikipedia.org)