• It involves the following computerized databases: NIG's DNA Data Bank of Japan (Japan), NCBI's GenBank (USA) and the EMBL-EBI's European Nucleotide Archive (UK). (wikipedia.org)
  • Other information about this group: The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community. (edu.au)
  • The contents of this collection is dynamic and will change over time as more data is deposited into the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt). (edu.au)
  • The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format. (nih.gov)
  • No BLAST database contains all the sequences at NCBI. (nih.gov)
  • The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. (wikipedia.org)
  • DDBJ is a member of International Nucleotide Sequence Database Collaboration (INSDC) . (nig.ac.jp)
  • 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)
  • They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. (plos.org)
  • The CDS/transcript files are usually associated with the proteome files in genome sequencing projects. (readthedocs.io)
  • Detecting the patterns of DNA sequence variants across the human genome is a crucial step for unraveling the genetic basis of complex human diseases. (psu.edu)
  • CDC used whole genome sequencing (WGS) analysis to link one case to contaminated opened powdered formula from the patient's home and the other to contaminated breast pump equipment. (medscape.com)
  • Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
  • This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)
  • However, the sheer volume of information generated by sequencing the exome or genome results in a variety of interpretive problems that complicate understanding of the results. (msdmanuals.com)
  • 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)
  • Since the 1990s, most of the world's major scientific journals have required that sequence data be deposited in an INSDC database as a pre-condition for publication. (wikipedia.org)
  • In many scientific journals, it is required to assign and to describe INSDC accession number for a nucleotide sequence on the research paper. (nig.ac.jp)
  • Once released, the nucleotide sequences submitted to INSDC including DDBJ are available for everyone . (nig.ac.jp)
  • 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)
  • The nucleotide sequence (2041 nucleotides) of a genomic region of herpes simplex virus type 1 (KOS strain) associated with virus-induced cell fusion has been determined. (johnshopkins.edu)
  • To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
  • Zebedee, SL & Lamb, RA 1989, ' Nucleotide sequences of influenza A virus RNA segment 7: A comparison of five isolates ', Nucleic acids research , vol. 17, no. 7, pp. 2870. (northwestern.edu)
  • Genetic relatedness of the isolates was characterized by multilocus sequence typing. (frontiersin.org)
  • Most of these CRAB isolates (77.62%) were classified as clone complex 92 (CC92), and sequence type (ST) 92 was the most prevalent STs, followed by ST195, ST136, ST843, and ST75. (frontiersin.org)
  • Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. (who.int)
  • There were two different mismatches in the probe target sites of the HA gene sequences of all isolates ( n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT-PCR isolates. (who.int)
  • Comparison of amino acid sequences of polypeptides encoded by mau genes from M. extorquens AM1, P. denitrificans, and Thiobacillus versutus shows that they have considerable similarity. (caltech.edu)
  • The nucleotide and amino acid sequences of the N (5') terminal region of gene G of bacteriophage phiphiX 174. (wikidata.org)
  • Design and test primers for this sequence using Primer-BLAST. (nih.gov)
  • The nested PCR primers used to isolate HCV sequences were designed and manufactured within CDC. (cdc.gov)
  • Using specific primers, mRNA fragments of genes encoding sesquiterpene lactones biosynthesis enzymes were amplified and their nucleotide sequences were determined. (academicjournals.org)
  • The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
  • Correlation between a coat protein amino-terminal sequence and a ribosome-binding DNA sequence from phiX 174. (wikidata.org)
  • Sequence analysis of mutant fii genes identified the 230-amino acid protein as the fii gene product. (duke.edu)
  • This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from Australian Mollusca, commonly known as molluscs, mollusks. (edu.au)
  • This tutorial demonstrates how to export ortholog groups from a previous Orthology search operation as protein and nucleotide sequences. (readthedocs.io)
  • To export the ortholog groups into protein sequence files (in Fasta format), a protein database of all input genomes must be provided. (readthedocs.io)
  • A protein database file is simply a Fasta file that contains all sequences used during the ortholog search procedure, with simplified headers. (readthedocs.io)
  • Your protein sequence files are ready to be used in the specified directory. (readthedocs.io)
  • Notice that TriFusion will set the same name for each taxon/species across the protein sequence files. (readthedocs.io)
  • The correspondence between each taxon sequence and the original header in the groups file will be written in the header_correspondance directory, for each protein sequence file. (readthedocs.io)
  • Refer to the previous Export into protein sequences section on how to set the protein database file. (readthedocs.io)
  • Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. (rcsb.org)
  • We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. (asm.org)
  • is a type of substitution in which the nucleotide change results in the replacement of one protein building block (amino acid) with another in the protein made from the gene. (medlineplus.gov)
  • Instead of causing a change in one amino acid, however, the altered DNA sequence results in a stop signal that prematurely signals the cell to stop building a protein. (medlineplus.gov)
  • Direct determination of DNA nucleotide sequences: structure of a fragment of bacteriophage phiX172 DNA. (wikidata.org)
  • The nucleotide sequence of a 1,854-base-pair DNA fragment carrying the fii region was determined. (duke.edu)
  • to point to the first base of every fragment respective to the original sequence. (mathworks.com)
  • We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. (plos.org)
  • When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
  • The nucleotide sequence of the PstI fragment was determined for the two mutants. (johnshopkins.edu)
  • Map 1: the map describes national viruses isolation, intratypic differentiation and nucleotide sequencing laboratories. (who.int)
  • The identity of the clone and the accuracy of the sequence was verified by direct aa sequencing of the tryptic peptides derived from the purified rat liver enzyme. (lu.se)
  • To address this question, we performed paired whole exome sequencing of donor and recipient DNA and single cell RNA sequencing (scRNA-seq) of 5 human kidney transplant biopsy cores. (biorxiv.org)
  • Exome sequences were used to define single nucleotide variations (SNV) across all samples. (biorxiv.org)
  • New and updated data on nucleotide sequences contributed by research teams to each of the three databases are synchronized on a daily basis through continuous interaction between the staff at each the collaborating organizations. (wikipedia.org)
  • Bioinformatics Biological database List of biological databases National Center for Biotechnology Information Sequence database Karsch-Mizrachi, I. (wikipedia.org)
  • The morphology of an isolated bacterial strain was found to be rod type, and the bacterium was identified as Lactobacillaceae species based on the GenBank database, through a phylogenetic analysis using the 16S rRNA sequence. (springeropen.com)
  • The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc. (bvsalud.org)
  • The human HapMap constructed by single nucleotide polymorphisms (SNPs) provides efficient sequence variation information that can speed up the discovery of genes related to common diseases. (psu.edu)
  • The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. (rcsb.org)
  • 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)
  • We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)
  • The mapping and sequence determination of the single site in phiX174am3 replicative form DNA cleaved by restriction endonuclease Pst I. (wikidata.org)
  • Direct determination of DNA nucleotide sequences. (wikidata.org)
  • Determination of restriction sites and the nucleotide sequence surrounding the relaxation site of ColE1. (musc.edu)
  • Small deletions remove one or a few nucleotides within a gene, while larger deletions can remove an entire gene or several neighboring genes. (medlineplus.gov)
  • Population-based Sanger sequencing has been shown to miss minor variants with a frequency below 20% 20 . (nature.com)
  • In this article, we present a generalized linear model for identifying specific nucleotide variants that encode complex human diseases. (psu.edu)
  • This process helps identify single or multiple nucleotide variations as well as areas of insertion or deletion. (msdmanuals.com)
  • For sequence submission to DDBJ, it is required for submitters to provide not only nucleotide sequence but also address of submitters and contact person , reference(s) (including primary citation ), names of source organisms, function, natures of genes, and so on (collectively means " registration information " of the entry). (nig.ac.jp)
  • Please note that mappings to Sequence Ontology (SO) are given in brackets () but should not be used as part of the value format. (insdc.org)
  • In principle, we cannot accept any sequence data from a student without whose advisers in names of submitter. (nig.ac.jp)
  • Due length of the sequences, data is available in text files to avoid truncation. (cdc.gov)
  • Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)
  • 2006. Sequencing for quasispecies analysis was done using the method described by Ramachandran et al. (cdc.gov)
  • 0 denotes a consensus sequence with no quasispecies analysis. (cdc.gov)
  • Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. (bvsalud.org)
  • Techniques of nucleotide sequence analysis that increase the scale of operations enabling an increase in the depth of coverage (number of copies) to which each polynucleotide is sequenced. (bvsalud.org)
  • The amino acid sequence of human rhodopsin, deduced from the nucleotide sequence of its gene, is 348 residues long and is 93.4% homologous to that of bovine rhodopsin. (nih.gov)
  • The nucleotide binding mode was corroborated by the replacement of critical residues. (rcsb.org)
  • The HCV RNA was isolated and sequenced either to determine the genotype of the isolated virus or to determine the viral quasispecies diversity within an infected individual. (cdc.gov)
  • The file may contain a single sequence or a list of sequences. (nih.gov)
  • Scholars@Duke publication: Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli. (duke.edu)
  • Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA seq. (erhard-lab.de)
  • Sequence-specific, single primer amplification and detection of PCR products for identification of hepatitis viruses. (cdc.gov)
  • An inversion changes more than one nucleotide in a gene by replacing the original sequence with the same sequence in reverse order. (medlineplus.gov)
  • Nucleotide clusters in deoxyribonucleic acids. (wikidata.org)
  • 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)
  • Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
  • Then use the BLAST button at the bottom of the page to align your sequences. (nih.gov)
  • Subject sequence(s) to be used for a BLAST search should be pasted in the text area. (nih.gov)
  • Find regions of similarity between these sequences and other sequences using BLAST. (nih.gov)
  • This can be helpful to limit searches to molecule types, sequence lengths or to exclude organisms. (nih.gov)
  • BLASTN programs search nucleotide subjects using a nucleotide query. (nih.gov)
  • The search will be restricted to the sequences in the database that correspond to your subset. (nih.gov)
  • 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)
  • The nucleotide sequence of the methylamine utilization (mau) gene region from Methylobacterium extorquens AM1 was determined. (caltech.edu)
  • The Committee concluded that additional work may be needed to assess the viability of the stocks held in VECTOR, and that further molecular characterization of additional strains may be valuable in helping to identify strains from which further DNA sequences could be determined. (who.int)
  • Finds sub-sequence or patterns in the sequence and highlights the matching region. (nih.gov)
  • Links in the FEATURES table will also highlight the corresponding region of the sequence. (nih.gov)
  • Lassa fe- Lassa virus in many more districts and states in en- ver is endemic in West Africa and has been reported demic countries of the West African sub-region and from Sierra Leone, Guinea, Liberia, and Nigeria4-7. (folkhalsomyndigheten.se)
  • a All sequencing reactions were performed in 96-well plates (Abgene, UK) in a DNA Thermal Cycler 9600 (Applied Biosystems, Warrington, UK) by using the following thermocycling conditions: 30 cycles of denaturation at 96°C for 10 s, annealing at 50°C for 5 s, and extension at 60°C for 2 min. (cdc.gov)
  • In some PCR reactions multiple sequences have identical nucleotide sequences, for example if five PCR products have identical sequences a 5 will be found in this column. (cdc.gov)
  • The purpose of these studies was to detect and determine the nucleotide sequences of mRNA enzymes germacrene A synthase (GAS, EC 4.2.3.23), germacrene A oxidase (GAO, EC 1.14.14.95) and costunolide synthase (COS, EC 1.14.13.120), involved in the biosynthesis of costunolide in A. glabella . (academicjournals.org)
  • The syntax is called INSDSeq and its core consists of the letter sequence of the gene expression (amino acid sequence) and the letter sequence for nucleotide bases in the gene or decoded segment. (wikipedia.org)
  • 2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription. (insdc.org)
  • 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)
  • When you wish to publicize your sequence through DDBJ, and your sequence is acceptable for DDBJ, you can submit your sequence to DDBJ, even if you have no plan to publication of any research paper related to the sequence. (nig.ac.jp)
  • In a deletion-insertion variant, at least one nucleotide is removed and at least one nucleotide is inserted. (medlineplus.gov)