Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987-2008 - Volume 16, Number 4-April 2010 -...
Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary ... Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria ... Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-80. DOIPubMed ... Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates. J Clin ...https://wwwnc.cdc.gov/eid/article/16/4/09-1361_article
Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5...
We performed several bioinformatics techniques to obtain more precise sequences using transcriptome assembly. In total, 42 MADS ... An expression analysis of the bamboo MADS-box genes in floral organs and leaves revealed that several key members are involved ... and some of the PeMADS sequences are fragmented and/or inaccurate. ... Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573.View ArticlePubMedPubMed ...https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-018-1394-2
Method for eliciting an immune response to human telomerase reverse transcriptase - Patent # 8709995 - PatentGenius
Leem, S. et al., "The human telomerase gene: complete genomic sequence and analysis of tandem repeat polymorphisms in intronic ... "Inverted terminal repeat sequence in the macronuclear DNA of Stylonychia pustulata," Gene, 1980, pp. 301-306, vol. 10. cited by ... Blackburn and Gall, "A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena," J ... Greider, C. and Blackburn, E. "A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis ...http://www.patentgenius.com/patent/8709995.html
Mapping of Hieracium (Asteraceae) chromosomes with genus-specific satDNA elements derived from next-generation sequencing data ...
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucl Acids Res 27:573-580CrossRefPubMedPubMedCentral ... Next-generation sequencing (NGS) has opened up new possibilities for high-throughput genome analysis. Here, we applied satDNA ... Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis suite. Nucl Acids Symp Ser 41:95-98 ... Raskina O, Brodsky L, Belyayev A (2011) Tandem repeats on an eco-geographical scale: outcomes from the genome of Aegilops ...https://link.springer.com/article/10.1007%2Fs00606-017-1483-y
Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors | BMC Genomics | Full Text
TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain. TLRs recognize and respond to ... Matsushima N, Ohyanagi T, Tanaka T, Kretsinger RH: Super-motifs and evolution of tandem leucine-rich repeats within the small ... Multiple sequence alignment, sequence similarity search and dot plot analysis. Multiple sequence alignments and sequence ... Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. ...https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-124
Construction, Expression, and Characterization of Thymosin Alpha 1 Tandem Repeats in Escherichia coli
Amino acid sequence analysis of thymosin α1 and polypeptide β1," Journal of Biological Chemistry, vol. 254, no. 3, pp. 987-995 ... The tandem repeats of proteins and peptides are studied widely and formidable progress has been made in this field. It was ... J. Varea, J. L. Saiz, C. López-Zumel et al., "Do sequence repeats play an equivalent role in the choline-binding module of ... C. A. Buscaglia, J. Alfonso, O. Campetella, and A. C. C. Frasch, "Tandem amino acid repeats from Trypanosoma cruzi shed ...https://www.hindawi.com/journals/bmri/2013/720285/
Manure From Antibiotic-Treated Livestock and MRSA | Clinical Pharmacy and Pharmacology | JAMA Internal Medicine | The JAMA...
Sequence analysis of the variable number tandem repeat in Staphylococcus aureus protein A gene: spa typing. In: DeLeo F, Otto M ... Sequence analysis of the variable number tandem repeat in Staphylococcus aureus protein A gene: spa typing. In: DeLeo F, Otto M ... All isolates were characterized by DNA sequence analysis of the protein A gene variable repeat region (spa typing).35 The spa ... Sensitivity analyses across time (eg, annual, seasonal, and 30-day exposure) and across space (eg, restricting analysis to ...https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/1738717
... and authenticated by short tandem repeat analysis.. BRAF DNA sequencing. BRAF mutation status was assessed by using next- ... Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis): Y. Narita, K. Okamoto ... Two att-site sequences and the MEK1 region were checked by sequencing. ... Sequencing data were produced by using a Genome Analyzer II (Illumina) and Standard Cluster Generation and 36 Cycle Sequencing ...http://mct.aacrjournals.org/content/13/4/823
The Complete Mitochondrial DNA Sequence of the Domestic Sheep ( Ovis aries) and Comparison with the Other Major Ovine Haplotype...
... was sequenced, together with part of the mtDNA of a specimen representing the other major O. arieshaplotype group.... ... Key words:Ovis aries- Mitochondrial DNA - Mitochondrial haplotypes - Tandem repeats - Nucleotide divergence - Sheep/cow ... The sequence data were included in analyses of intraspecific ovine molecular differences, molecular comparisons with bovine ... due to heteroplasmy caused by the occurrence of different numbers of a 75-nt-long tandem repeat in the control region. ...https://rd.springer.com/article/10.1007/PL00006401
Patent US20020150909 - Automated information processing in randomly ordered arrays - Google Patents
Previous work utilized short tandem repeats (STRs) as polymorphic positional markers; however, recent focus is on the use of ... IBL3 and IBL4 gives a sequence of AA; IBL1, IBL2, and IBL3 shows the sequence AT; IBL1, IBL3 and IBL4 gives the sequence TA, ... Image processing and analysis of array data. US7356184. May 23, 2006. Apr 8, 2008. Xiongwu Xi. Analysis of array/assay data ... The target sequence may be a portion of a gene, a regulatory sequence, genomic DNA, cDNA, RNA including mRNA and rRNA, or ...http://www.google.com/patents/US20020150909?dq=6,219,045
US6764822B1 - DNA typing by mass spectrometry with polymorphic DNA repeat markers - Google Patents
... such as microsatellites and short tandem repeats, and to DNA sequences provided as primers for the analysis of DNA tandem ... is more specifically directed to the use of mass spectrometry to detect length variation in DNA nucleotide sequence repeats ( ... nucleotide repeat polymorphisms at specific loci on specific chromosomes. ... simple sequence repeats, short tandem repeats and variable nucleotide tandem repeats. As used herein, the term "DNA tandem ...https://patents.google.com/patent/US6764822
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences | BMC Bioinformatics ...
We show that RIP has affected different members of the S. nodorum rDNA tandem repeat to different extents depending on their ... The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, ... Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these ... a software tool for the automated analysis of RIP in fungal genomic DNA repeats, which performs both RIP index and alignment- ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-478
Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans...
110.Benson G: Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res 1999, 27(2): 573-580. 111.Finn RD, ... All three grow well in media rich in glutamic acid . Multilocus sequence typing and other molecular analyses [28-30] have ... The list of gene sequences used to build the tree is given in additional file 6 (Table S6). The Tandem Repeat Finder program [ ... 9 of 25 Figure 3 Maximum likelihood tree of Xanthomonas pth genes The sequences used to build the tree had their tandem repeat ...http://ufdc.ufl.edu/AA00008952/00001
Genome diversification within a clonal population of pandemic Vibrio parahaemolyticus seems to depend on the life circumstances...
Whole genome sequence comparison of eight independent isolates of this population from mussels or clinical cases (from ... Here, genomics analyses of isolates from this rapidly expanding clonal population offered an opportunity to observe the ... Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat ... For analysis of the sequences, the single-end raw reads from the Ion Torrent were converted into FASTQ format using sff2FASTQ ...https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1385-8
Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola | BMC...
The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using ... BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. ... Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for ... Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306 ...https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-015-0562-x
Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house...
Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of intermingled ... patterns of variant repeats along the repeat array. To reconstruct the genealogy of these arrays of variable length, the ... Tamaki K, Jeffreys AJ: Human tandem repeat sequences in forensic DNA typing. Leg Med (Tokyo). 2005, 7: 244-250.View Article ... Recently, however, development of new algorithms specifically designed to treat tandem repeat data has made analysis of large ...https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-5-r80
Optimization of sequence alignment for simple sequence repeat regions | BMC Research Notes | Full Text
... or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer ... The whole sequence length was changed after the new algorithm was applied from 479 bp to 539 bp. The cluster analysis resulted ... The sequence case C contained a compound SSR of TA, CA, and CG tandem repeats representing 35% of the whole sequence. Applying ... Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences with a period of from 1 to 6 base pairs ...https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-4-239
December 2000 - American Renaissance
This is because there are many DNA sequences (such as STRs, or Short Tandem Repeats, and SNPs, or Single Nucleotide ... These data are therefore a virtually irrefutable demonstration of the reality of race - a purely statistical analysis of allele ... Analysis of Y-markers will automatically concentrate only on the male DNA. ... analysis of mtDNA transmitted in the maternal line might tell a different story. The authors point out that "comprehensive ...https://www.amren.com/archives/back-issues/december-2000/
United Kingdom National DNA Database - Wikipedia
Only patterns of short tandem repeats are stored in the NDNAD - not a person's full genomic sequence. Currently the ten loci of ... The data held on the NDNAD is owned by the police authority which submitted the sample for analysis. The samples are stored ... Any NDNAD hits obtained are reported directly to the police force which submitted the sample for analysis. The NDNAD is widely ... a position backed up by the fact that the majority of the searches would have been repeated, and that there are not 1 trillion ...https://en.wikipedia.org/wiki/United_Kingdom_National_DNA_Database
Patent US7285384 - Parallel genotyping of multiple patient samples - Google Patents
The patient beads can then be used in a variety of target analyte analyses. ... or other sample analysis) of multiple patients by direct sample immobilization onto microspheres of an array. ... Nucleic acid analysis using sequence-targeted tandem hybridization. US6268148. 15 Nov 1999. 31 Jul 2001. Francis Barany. ... Previous work utilized short tandem repeats (STRs) as polymorphic positional markers; however, recent focus is on the use of ...http://www.google.ca/patents/US7285384
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Genotypically identical strains (sequence type ST8, spa-type t024, MLVA-type 4698, enterotoxin A FRI100) were isolated in 10 ... Whole genome sequencing resulted in phylogenetic clustering which concurred with traditional typing while simultaneously ... Non-enterotoxigenic strains with livestock-associated sequence type ST398 were isolated from three food items and two members ... food and catering staff were characterised and compared using traditional typing methods and whole genome sequencing. ...http://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2015.20.45.30059
US7005050B2 - Electrophoresis in microfabricated devices using photopolymerized polyacrylamide gels and electrode-defined...
67:3676-3680, 1995) and short tandem repeats (Schmalzing, D., et al., Proc. Natl. Scad. Sci, USA 94:684-688, 1998) using a ... Miniaturized total analysis systems for biological analysis. Waters et al. 1998. Multiple sample PCR amplification and ... A sequence of video images from this separation are shown in FIGS. 8. (a-d). FIGS. 8. a and 8 b shows fluorescently labeled 100 ... Analysis US20040112751A1 (en) * 2002-08-26. 2004-06-17. Jongyoon Han. Multidimensional electrophoresis and methods of making ...https://patents.google.com/patent/US7005050B2/en
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis | BMC Bioinformatics | Full Text
... data-driven and protocol-driven analysis approaches. The prototype of AnaBench, managed by a team at the Université de Montréal ... and memorization of numerous parameters and multi-step analysis procedures. In this paper, we present the design and ... Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of ... implementation of AnaBench, an interactive, Web-based bioinformatics Ana lysis workBench allowing streamlined data analysis. ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-63
DynamicOryzaGenomes: Repetitive DNA Sequences as Genome Modeling Agents | SpringerLink
However, little is known about how these sequences originate, evolve and function in context of ... Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. ... Volfovsky N, Haas B, Salzberg S. A clustering method for repeat analysis in DNA sequences. Genome Biol. 2001;2: ... tandem repeats can diverge and disperse, and the dispersed repeats can cluster together which can be differentiated by FISH. ...https://link.springer.com/article/10.1007%2Fs12284-010-9054-7
Frontiers | A Virus-Derived Stacked RNAi Construct Confers Robust Resistance to Cassava Brown Streak Disease | Plant Science
... sequences of CBSV and UCBSV fused in tandem. Northern blots using probes specific for each CP sequence were performed to ... sequences of CBSV and UCBSV fused in tandem. Northern blots using probes specific for each CP sequence were performed to ... Transgenic plant lines were generated expressing an inverted repeat construct (p5001) derived from coat-protein (CP) ... Transgenic plant lines were generated expressing an inverted repeat construct (p5001) derived from coat-protein (CP) ...https://www.frontiersin.org/articles/10.3389/fpls.2016.02052/full