• Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes , which is closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni , was determined. (pnas.org)
  • The W. succinogenes genome sequence has been assigned EMBL accession no. (pnas.org)
  • Previous phylogenetic analyses of 16S rRNA, recA , gyrB , rpoB , and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. (springer.com)
  • Community-wide analysis of microbial genome sequence signatures. (nih.gov)
  • Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. (nih.gov)
  • Availability of the reference human genome sequence enabled the generation of oligonucleotide probes and short sequence markers (SNPs) mapped to specific chromosome positions that could then be used to generate microarray platforms to analyze DNA from specific patients to search for genomic copy number variants and genomic structural variants. (frontiersin.org)
  • Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor ∼706,000 years ago, and that the human and Neanderthal ancestral populations split ∼370,000 years ago, before the emergence of anatomically modern humans. (sciencemag.org)
  • Our laboratory is analyzing a large amount of human genome sequence data (whole genome, exome, and RNA-seq) by using cutting-edge next-generation sequencers and performing highly innovated informatics approach, and is providing basic genome information to clarify the relationship between genetic variations and cancer, human diseases, and drug response. (riken.jp)
  • 1. Marthaler D, Jiang Y, Otterson T, Goyal S, Rossow K, Collins J. Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States. (cdc.gov)
  • Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. (usda.gov)
  • At the NHGRI-DOE five-year planning meeting (May 1998), participants recommended rapid production of a draft' version of the human genome sequence, based on mapped, large-insert clones. (mit.edu)
  • Whole genome sequence of the human WNV isolate showed close phylogenetic relatedness to the Italy-1998-WNV strain and to other WNV strains recently isolated in Europe, with the new acquisition of the NS3-Thr249Pro mutation, a trait associated with avian virulence, increased virus transmission, and the occurrence of outbreaks in humans. (eurosurveillance.org)
  • By applying emotif to all of these alignments, we have generated a database called identify , which contains more than 50,000 sequence motifs with specificities varying from one expected false positive prediction in 10 5 tests to as low as one expected false positive prediction in 10 10 tests. (pnas.org)
  • and to automatically construct large multiple alignments (i.e. with an effectively unlimited number of sequences) using a profile representative of a sequence family. (ubuntu.com)
  • In this lecture I will focus on the basic models and how to formulate a dynamical programming algorithm that can calculate the probability of 2 homologous sequences and define a distribution on all possible alignments. (edu.au)
  • Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. (umd.edu)
  • Whether performing reference-guided alignments, de novo assembly, variant calling, or SNP analyses, Sequencher has the tools you need to get results. (genecodes.com)
  • Easily use consensus sequences from the Project Window as a reference sequence for NGS alignments for hybrid sequencing projects. (genecodes.com)
  • The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows-Wheeler indexes, graph algorithms and a number of advanced omics applications. (cambridge.org)
  • High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. (nih.gov)
  • Probably the most important achievement of ChIP-Seq is the population-level analysis of interactions between protein and DNA. (news-medical.net)
  • These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. (springer.com)
  • The new service will be offered on the Illumina GA II and will include the following applications: Shotgun Sequencing, ChIP Seq, mRNA Seq and small RNA Seq. (fiercebiotech.com)
  • Annotation and Analysis. (pnas.org)
  • Inappropriate use of sequence analysis procedures may result in numerous errors in genome annotation (we have already touched upon this subject in the previous chapter and further discuss it in Chapter 5). (springer.com)
  • Suppose you have sequence(s) that you want to analyze using a HMMER-based profile HMM database like Pfam ( http://pfam.sanger.ac.uk ). (ubuntu.com)
  • This webinar will discuss a comprehensive end-to-end workflow for soil metagenomic shotgun sequencing that offers an unbiased alternative to amplicon-based approaches to assess the composition of culture-free microbial communities and predict functional profiles. (genomeweb.com)
  • Platforms utilized include Affymetrix GeneChip® and GeneTitan®, Applied Biosystems' Taqman, Fluidigm's Biomark and Access Array Systems, Illumina BeadChip® and Genome Analyzer, NanoString Technologies nCounter® Analysis System, RainDance Technologies RDT 1000 and, in the near future, the Pacific Biosciences™ PacBio RS. (fiercebiotech.com)
  • Indexed libraries that are ready for Illumina sequencing can be prepared in less than 4 hours using the SMARTer Stranded RNA-Seq Kit protocol. (clontech.com)
  • Integrated with Illumina sequencing -Incorporates indexes and Illumina adapters in the workflow. (clontech.com)
  • Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. (genetics.org)
  • Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. (genetics.org)
  • Sequence analysis of the protective and hypertensive BP loci revealed 1433 and 2063 variants between Dahl salt-sensitive/Mcwi and Brown Norway rats, respectively. (ahajournals.org)
  • Sequence comparison among Dahl salt-sensitive, Dahl R, and Brown Norway reduced the number of candidate variants in the 2 BP loci by 42% for further study. (ahajournals.org)
  • A 24-loci 'mycobacterial interspersed repetitive unit-variable-number tandem-repeat' (MIRU-VNTR) genotyping analysis was performed on all culture-positive, laboratory-confirmed isolates at the National Reference Centre for Mycobacteriology of the National Microbiology Laboratory in Winnipeg, Manitoba. (medindia.net)
  • The report offers a quantitative analysis from 2017 to 2023, which is expected to enable the stakeholders to capitalize on prevailing market opportunities. (openpr.com)
  • Cellular heterogeneity plays a critical role in systems and pathologies, but many genomic analysis techniques derive their findings from multicellular samples, potentially burying key information from individual cells or rare subsets. (the-scientist.com)
  • The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa , a copper-tolerant fungus that causes brown rot decay of wood. (usda.gov)
  • Nucleotide sequence analysis, which control investigation. (cdc.gov)
  • Investigators of acute HIV infection in persons with recent health care exposure and no known risk factors for HIV might consider the possibility of health care-associated transmission and conduct nucleotide sequence analysis. (cdc.gov)
  • Among persons with known HIV infection who had hospitalization dates overlapping those of patient A, one person (patient B) had an HIV strain highly similar to patient A's strain by nucleotide sequence analysis. (cdc.gov)
  • Nucleotide sequence analysis, which is increasingly used for detecting HIV clusters (i.e., persons with closely related HIV strains) and to inform public health response ( 2 , 3 ), might also be used to identify possible health care-associated transmission of HIV to someone with health care exposure and no known HIV risk factors ( 4 ). (cdc.gov)
  • Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. (sciencemag.org)
  • The programs can be 'piped' into one another, allowing the simultaneous identification of promoters, coding exons and repetitive sequence using one command line. (bio.net)
  • It was found that 4-5X coverage is enough to give the maximum ability to find exons in the draft sequence (~90% of exons were found in the Blast comparison, ~70-80% with Genscan). (mit.edu)
  • It was clear that the utility of draft sequence will depend on the uses to which it is put, in particular on the size of the sequence feature (e.g., exons vs. long-range duplications) one is interested in studying. (mit.edu)
  • During the past summer, the NHGRI-supported sequencing centers assessed strategies to generate a shotgun product that would constitute a working draft' of the human genome. (mit.edu)
  • Sequencing centers produced several versions of possible working drafts, using a sample of four BAC clones containing inserts whose finished sequence is already known and annotated. (mit.edu)
  • The DNA sequence and comparative analysis of human chromosome 5. (uniprot.org)
  • Clustering and comparative analysis of miRNA read frequencies showed that normal breast samples were separated from most noninvasive ductal carcinoma in situ and invasive carcinomas by increased miR-21 (the most abundant miRNA in carcinomas) and multiple decreased miRNA families (including miR-98/let-7), with most miRNA changes apparent already in the noninvasive carcinomas. (aacrjournals.org)
  • The following chap- ters describe the process of aligning multiple sequences in order to assemble overlapping fragments into sequence contigs to compare similar sequences from different sources. (springer.com)