• Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in a genome. (researchsquare.com)
  • Sequences repeated in tandems (microsatellites) are used for parentage testing. (genomia.cz)
  • These microsatellites contain sequences repeated in tandems from two to seven base pairs. (genomia.cz)
  • Microsatellites (Short sequence repeats, SSRs, Short tandem repeats): are short (1-6bp) repeating sequences in genetic code. (flashcardmachine.com)
  • Microsatellites were observed only in euchromatin regions, whereas the (TTAGG) 6 repeats were found at telomeric sites in both groups. (karger.com)
  • These sequences, also called microsatellites, are a class of genetic markers consisting of tandem sequence repeats with a size of two to seven base pairs. (genomia.cz)
  • Microsatellites are small DNA sequences made up of repeating units. (vajiramandravi.com)
  • Although NanoSTR needs further optimization and development, it is useful as an analytical method for the detection of STR loci by nanopore sequencing. (researchsquare.com)
  • These highly individual-specific number of repeats and the abundance of motifs have contributed to the polymorphism of STR loci. (researchsquare.com)
  • 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)
  • To that end, several short tandem repeat loci were selected for targeted sequencing, and a bioinformatic pipeline for analyzing the sequence data was developed. (ojp.gov)
  • Our search of the Rd genome sequence identified 9 novel loci with multiple (range 6-36, mean 22) tandem tetranucleotide repeats. (jcvi.org)
  • In human genome contain a large number of DNA segments of tandemly repeated sequences as VNTR (Variable number of tandem repeats) loci. (medline.ru)
  • In order to obtain population data in the Lithuania, allele frequencies and genotype distribution of two polymorphic loci (YNZ22 and Ig-J H ). The Ig- J H VNTR locus, situated on chromosome 14, the polymorphism detected using PCR consists of 13 alleles, ranging in length from 420 bp to 1020 bp with a 50 bp core sequence. (medline.ru)
  • BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • They are also known as short tandem repeats (STRs) or simple sequence repeats (SSRs). (vajiramandravi.com)
  • CareDx will be on hand to display its leadership in serving European laboratories, researchers, and clinicians with its best-in-class product portfolio of next-generation sequencing (NGS) based AlloSeq* products, which enables best-in-class care both pre- and post-transplantation. (portada-online.com)
  • Comparison of Next-Generation Sequencing and Short-Tandem Repeats to Monitor Chimerism Analysis. (portada-online.com)
  • Detection of HLA-A and HLA-J haplotype diversity from next-generation sequencing data in commercially available samples. (portada-online.com)
  • PulseNet: Entering the Age of Next-Generation Sequencing. (cdc.gov)
  • Nanopore sequencing is an evolving third/fourth generation sequencing technology for direct detection of nucleotide sequences with kb or even Mb base pairs (7)(8) . (researchsquare.com)
  • We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
  • The nucleotide sequences of Serine-Rich Entamoeba histolytica Protein (SREHP) gene have already exhibited stable and significant polymorphism in the gene studies. (scialert.net)
  • The first nucleotide sequences have been shown the stable and significant polymorphism in the Strain Specific Gene (SSG) and the Serine-Rich E. histolytica Protein (SREHP) gene. (scialert.net)
  • Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)
  • To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. (karger.com)
  • To determine the genetic profile, tandem repetitive sequences (STR) are used. (genomia.cz)
  • A local high frequency of microhomologies, macrohomologies, tandem repeats, and repeat/repetitive sequences contribute to a high rate of nonallelic homologous recombination involving NEMO , resulting in the development of de novo deletion mutations. (medscape.com)
  • 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)
  • Human microbiome analysis can be used in combination with traditional human DNA analysis techniques such as short-tandem-repeat sequencing and single nucleotide polymorphism analysis to provide more robust results in cases where people are suspected of having been involved with bioterrorism or biocrime. (news-medical.net)
  • Students will gain knowledge in human genetic variability and DNA repeats, and skills in analyzing high-throughput sequencing data, algorithm design and testing, and database development. (bu.edu)
  • In some cases, tandem repeats can serve as genetic markers to track inheritance in families. (genome.gov)
  • Ghosh reported 5 different SREDP sequencing patterns from 5 isolates and showed high genetic variation among the E. dispar in compare with E. histolytica (Ghosh et al . (scialert.net)
  • In the present study, the genetic variability of E. dispar strains based on the SREDP gene locus was analyzed using RFLP-nested PCR and sequencing of the obtained genes. (scialert.net)
  • The bioinformatician works with bioinformatic analyses of genetic data from high throughput genetic sequencing from patients and families with Parkinson disease, dementia, other movement disorders and cerebrovascular disorders. (lu.se)
  • Tandem-Genotypes requires data preprocessing steps such as LAST alignment and establishment of a genomic background database, and histograms are needed to assist STR genotyping. (researchsquare.com)
  • In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona , and allotetraploid E. oryzicola ) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. (nature.com)
  • In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
  • The Benson lab develops algorithms and software for biological sequence comparison and repeat detection in genomic sequences. (bu.edu)
  • Ultimately, the rapid development of sequencing technologies allowed studies at the genomic level, augmenting the resolution of association with environment factors. (intechopen.com)
  • The potential application of our method includes annotation of new genomic sequences and motif discovery. (biomedcentral.com)
  • Therefore, to address the growing volumes of available genomic sequence, a number of algorithms that identify putative cis-regulatory modules and transcription factor binding sites using evolutionary comparisons, whole-genome data, and known descriptions of transcription factor binding sites, have been successfully developed. (biomedcentral.com)
  • We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences. (biomedcentral.com)
  • Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. (bvsalud.org)
  • While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. (researchgate.net)
  • Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
  • Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. (biomedcentral.com)
  • This is an actively progressing area, as more and more sequenced genomes appear. (biomedcentral.com)
  • While the reduction in the cost of WGS is making sequencing more affordable in lower- and middle-income countries (LMICs), public health laboratories in these countries seldom have access to bioinformaticians and system support engineers adept at using the Linux command line and complex bioinformatics software. (researchgate.net)
  • Article: An integrative approach for codon repeats evolutionary analyses Journal: International Journal of Data Mining and Bioinformatics (IJDMB) 2012 Vol.6 No.4 pp.369 - 381 Abstract: The relationship between genome characteristics and several human diseases has been a central research goal in genomics. (inderscience.com)
  • Over recent decades, advances in technologies such as massive parallel sequencing, atomic force microscopy, mass spectrometry and bioinformatics now enable high-level microbial characterization for various applications including the identification of perpetrator(s), body fluid assessment, and the tracking of infectious agents. (news-medical.net)
  • ATRX can bind the variable number of tandem repeats (VNTR) sequence in the promoter region of the α-globin gene cluster. (jascoinc.com)
  • The VNTR sequence, which contains the potential G-quadruplex-forming sequence CGC(GGGGCGGGG)n, is involved in the downregulation of α-globin expression. (jascoinc.com)
  • This project will develop new algorithmic and statistical methods to permit detection of longer VNTR repeats and the use of longer read sequencing technologies. (bu.edu)
  • Short tandem repeats (STRs) are widely present in the human genome. (researchsquare.com)
  • For example, NanoSatellite directly analyzes STRs based on electric current distribution, and the accuracy of analysis depends heavily on the stability of the sequencing current and the precision of the basecalling model. (researchsquare.com)
  • We therefore developed NanoSTR as a method for detecting target STRs based on nanopore sequencing. (researchsquare.com)
  • 2018) using expressed sequence tag-short tandem repeats (EST-STRs) markers. (matis.is)
  • Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
  • However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. (inderscience.com)
  • DNA repeats identify novel virulence genes in Haemophilus influenzae. (jcvi.org)
  • The third subfamily, with little conserved amino acid sequences around the NPA boxes, include 'superaquaporins' (S-aquaporins). (wikipedia.org)
  • From positive samples for msp1α snPCR, samples were analyzed for the amino acid sequences of this gene. (scielo.br)
  • However, sequencing revealed only five animals, including the bovine which died, with a similarity of the amino acid sequences with AmRio 2 strain of A. marginale . (scielo.br)
  • NanoSatellite: Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. (logosbio.com)
  • The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
  • Further characterization of the lgtC gene showed that it was involved in phenotypic switching of a lipopolysaccharide epitope and that this variable expression was associated with changes in the number of tetranucleotide repeats. (jcvi.org)
  • In NSW, Salmonella isolates are referred to Pathology West - Institute for Clinical Pathology and Medical Research, the state reference laboratory, for further characterization, including serotyping and DNA sequence-based subtyping with multiple-locus variable-number tandem repeats analysis (MLVA). (who.int)
  • However, there are few methods for STR detection based on nanopore sequencing due to the challenges posed by the sequencing principles and the data characteristics of nanopore sequencing. (researchsquare.com)
  • NanoSTR can be used for STR detection and genotyping based on long-read data from nanopore sequencing with improved accuracy and efficiency compared with other existing methods, such as Tandem-Genotypes and TRiCoLOR. (researchsquare.com)
  • This method adds to the toolbox for nanopore-based STR analysis and expands the applications of nanopore sequencing in scientific research and clinical scenarios. (researchsquare.com)
  • There are a few methods for STR identification based on nanopore sequencing, and the representative software are Tandem-Genotypes (11) , NanoSatellite (12) , STRique (13) , etc. (researchsquare.com)
  • In terms of data characteristics, NanoSTR effectively avoids the non-random sequencing errors and unexpected insertions-deletions (indels) associated with nanopore sequencing (8)(9) and thus improves the efficiency of sequencing data utilization, the detection rate of STR genotypes, and the accuracy of STR profiling. (researchsquare.com)
  • Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing. (mpg.de)
  • Nanopore SimulatION - a raw data simulator for Nanopore Sequencing. (mpg.de)
  • A tandem repeat is a sequence of two or more DNA bases that is repeated numerous times in a head-to-tail manner on a chromosome. (genome.gov)
  • Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. (biomedcentral.com)
  • Tandem repeats, which display a greater propensity to mutate, and are often hypomethylated in cancer patients, have never been investigated in individuals exposed to PM. We measured methylation of three tandem repeats (SATα, NBL2, and D4Z4) by polymerase chain reaction-pyrosequencing on blood samples from truck drivers and office workers (60 per group) in Beijing, China. (nih.gov)
  • RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data. (mpg.de)
  • The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering. (inderscience.com)
  • The lab has developed an analysis tool, VNTRseek, to identify VNTRs, using high-throughput sequencing data, but it is limited to those TRs that fit within a sequencing read. (bu.edu)
  • However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases. (syr.edu)
  • Identification of a salmonellosis outbreak by means of molecu- variable number tandem repeat analysis type in Australia, 2014. (who.int)
  • In September 2015, the South Western Sydney (SWS) Public Health Unit was notified of a cluster of Salmonella Typhimurium (STm) cases with a common multiple-locus variable-number tandem repeats analysis (MLVA) pattern. (who.int)
  • However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • The number of repeats at a certain microsatellite locus might vary greatly between people in a population because microsatellite DNA is highly variable. (vajiramandravi.com)
  • The alleles of STR locus change according to the number of repeats of the given sequence motive. (genomia.cz)
  • For example, one copy of a specific short tandem repeat (STR) region might have 10 repeats, while the other copy might have 11 repeats. (ojp.gov)
  • Comparatively short sequences (several hundred to several thousand base pairs, depending on thespecies) upstream or downstream of the transcription start site often play a major role in the regulation of gene expression. (biomedcentral.com)
  • New DNA Commission recommendations The DNA Commission of the ISFG has just released the recommendations on Short Tandem Repeat sequence nomenclature! (isfg.org)
  • Sequence alterations, copy number variants and short tandem repeats in human DNA can be detected. (lu.se)
  • It was postulated the moderate effect of crowding on Histatin 5 was due to its short sequence-length. (lu.se)
  • The focus is understanding the occurrence and functional effects of tandem repeats (TRs), and especially, those with variable copy number, also known as variable number of tandem repeats (VNTRs). (bu.edu)
  • The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a National Reference Laboratory in a smaller country. (applied-maths.com)
  • Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. (cdc.gov)
  • In practice, however, the high error rate and special data characteristics of long-read sequencing have limited the efficient identification of STR polymorphisms, and therefore, further evaluation of the analytical methods is required (9)(10) . (researchsquare.com)
  • This project involves the development of statistical tools and software for jointly analyzing microbial and host data from sequencing experiments, in order to determine community content, microbe-microbe interactions, and host-microbe relationships. (bu.edu)
  • Microbial DNA sequence data will be collected from soils obtained through a national sampling initiative - the National Ecological Observatory Network (NEON). (bu.edu)
  • These data indicate the rapidity, economy, and completeness with which whole genome sequences can be used to investigate the biology of pathogenic bacteria. (jcvi.org)
  • Sequencing Data Discovery with MetaSeek. (cdc.gov)
  • Besides, NanoSTR also showed 86.36% and 73.48% concordance using the standard samples 9948 and 2800M with MinION sequencing platform, respectively. (researchsquare.com)
  • The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)
  • Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. (cdc.gov)
  • Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
  • Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
  • Harmonization of whole-genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci. (applied-maths.com)
  • Measuring tandem-repeat hypomethylation in easy-to-obtain blood specimens might identify individuals with biological effects and potential cancer risk from PM exposure. (nih.gov)
  • 4. Expert opinion on whole genome sequencing for public health sur- ratory surveillance. (who.int)
  • From those isolates, six distinct DNA patterns were observed after PCR-RFLP of the nested PCR, whereas sequencing showed 8 different patterns among the isolates. (scialert.net)
  • In contrast, marine bony fish harbor more tandem repeats than freshwater species. (syr.edu)
  • Sequence evolution of the pseudoautosomal region after the split between the avian and mammalian lineages, and leading up to extant mammalian species, involved the formation of several evolutionary strata mediated by recombination suppression between the sex chromosomes [ 18 , 19 , 20 ]. (biomedcentral.com)
  • This study addressed the role of DEP-1 for regulation of the acute myeloid leukemia (AML)-related mutant FLT3 internal tandem duplication (ITD) protein. (nih.gov)
  • The polymorphism of the Serine-Rich Entamoeba dispar Protein (SREDP) gene among 8 isolates obtained from Iranian cyst carriers were analyzed by a nested PCR-RFLP followed by sequencing of the PCR products. (scialert.net)
  • These tetranucleotide repeat sequences were also shown to be present in two other epidemiologically different H. influenzae type b strains, although the number and distribution of repeats was different. (jcvi.org)
  • To evaluate this pipeline, DNA from pairs of individuals were mixed at different ratios (1−1, 1−9) and sequenced with different starting amounts of DNA (10, 1 and 0.1 ng). (ojp.gov)
  • The sequences are about 300 base pairs long and are repeated several thousand times throughout the genome. (ojp.gov)
  • These repeating units, which are typically 1-6 base pairs in length, are repeated in tandem, and the amount of repetitions varies between individuals. (vajiramandravi.com)
  • The number of repeat units differs between individuals, resulting in highly complex allele polymorphisms. (researchsquare.com)
  • Complete rRNA sequence, arrangement of tandem repeated units and phylogeny of Nosema fumiferanae from spruce budworm, Choristoneura fumiferana (Clemens). (gc.ca)
  • The repeat-containing region of the SREDP was found extensively polymorphic in size, number and order of repeat units. (scialert.net)
  • However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. (nih.gov)
  • All colonies, regardless of the nucleotide sequence of rpsA , were found to be sensitive to all of the drugs tested except for ethambutol. (frontiersin.org)