bar coded multiplexed sequencing of targeted dna regions using the illumina genome analyzer
Báo cáo y học: " Ultrafast and memory-efficient alignment of short DNA sequences to the human genome" pdf
... 'double indexing' Two indices of the genome are created: one containing the BWT of the genome, called the 'forward' index, and a second containing the BWT of the genome with its character sequence ... explanation of how the reverse complement is incorporated The first 28 bases on the high-quality end of the read are termed the 'seed' The seed consists of two halves: the 14 bp on the high-quality ... (Figure 1c) calculates the range of matrix rows beginning with successively longer suffixes of the query At each step, the size of the range either shrinks or remains the same When the algorithm completes,...
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Báo cáo hóa học: " Stretching and immobilization of DNA for studies of protein–DNA interactions at the single-molecule level" ppt
... oligonucleotide to the DNA As discussed earlier, the force on the DNA can be obtained from the transverse Brownian motion of the free end of the DNA using the equipartition theorem van Oijen et ... displacement on one of the traps, while monitoring the coupled motion of the other bead (Fig 3C) The RNAP DNA interaction was identified through changes in the ‘‘stiffness’’ of the response of the second ... about in the following way First, a free end of the DNA sticks to the hydrophobic substrate, presumably due to its affinity to the exposed hydrophobic bases at the end of the DNA; then the DNA molecule...
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Báo cáo sinh học: " Chromosomal localization and activity of nucleolar organizer regions in the dog" pot
... made the development of the physical mapping of the canine genome possible The objective of the present study was the chromosomal localization of NORs in the dog karyotype and the analysis of their ... 13q [8] The analysis of their activity showed that the mean number of silver stained NORs was 5.2, but the modal number was [17] The highest number of NORs was found in the karyotype of the blue ... karyotype, a NOR occurred also in the terminal part of the long arm of the Y chromosome A detailed analysis of the silver deposit distribution on the chromosomes of 27 individuals showed that all...
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báo cáo khoa học: "Genomic profiling of plastid DNA variation in the Mediterranean olive tree" pdf
... the organelle genomes (i.e., plastid DNA - cpDNA - and mitochondrial DNA mtDNA) for six major reasons: (i) these genomes are usually uniparentally inherited (either from the mother or the father) ... challenging, limiting the applications of such an approach In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with ... molecular variation at these non-synonymous sites would deserve the design of an experiment to test their origin and their adaptive significance Development of cpDNA markers The low cpDNA substitution...
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Báo cáo y học: "Taxonomic distribution of large DNA viruses in the sea" pptx
... dividing the cumulated size of reads contributing to the contig by the size of the contig Relative abundance of PolBs For the analysis of the relative abundance of PolB sequences, we used the same ... positions for each of the GOS PolB fragments We aligned, one by one, each of the PolB fragments on the reduced reference MSA using the T-Coffee profile method Based on the resulting profile MSA containing ... Additional data file show the taxonomic distribution of the GOS PolB fragments The largest fraction of the PolB fragments was mapped on the phage group Of 866 cases of mapping within the phage group,...
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Báo cáo khoa học: Functional analysis of pyrimidine biosynthesis enzymes using the anticancer drug 5-fluorouracil in Caenorhabditis elegans docx
... biosynthesis pathways Two pathways allow the conversion of 5-FU to FdUMP in humans The C elegans genome has homologs for the enzymes in these pathways Humans show redundancy of pyrimidine synthesis ... 5¢-deoxy-5-fluorouridine (5dFUR) to further examine the function of UPP-1 in the pyrimidine biosynthesis pathway 5dFUR is converted to 5-FU by UP and TP [9] The effects of 5dFUR in the upp-1 mutant are questionable, ... homologs for most of them in C elegans To explore the functional relationships of these pyrimidine biosynthesis enzymes using 5-FU, we used FEBS Journal 276 (2009) 4715–4726 ª 2009 The Authors Journal...
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Báo cáo khoa học: DG-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome pot
... shown The positions of slr1667 and slr1668 are shown at the top; the arrows represent the actual binding site of the slr1667–slr1668 operon The A binding site upstream of the operon has the lowest ... increased when the concentration of SYCRP1 was increased The increment varied with the DNA sequence to which the SYCRP1 bound The intensity of the complex band decreased with the increase in ... Figure shows the procedure for the DDG-based prediction The binding affinity of SYCRP1 to a fragment of 16 bp is estimated as the sum of the DDG values at each position The window of 16 bp was...
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Báo cáo sinh học: " The 3'''' sequences required for incorporation of an engineered ssRNA into the Reovirus genome" pot
... possess the tetranucleotide GCUA- at their 5' ends and the pentanucleotide -UCAUC at the 3' ends of their plus strands This conservation of nucleotides is also present in the ssRNAs of the other ... sequence but not show the 3' end of the ssRNA The 3' sequence of these ssRNAs is shown in its entirety from the CAT stop codon to the authentic reovirus 3' terminus directly below the 5' ssRNA sequences ... intermediates using the ssRNAs generated from the sequence-substitution cDNA templates outlined in Table 2, using the reovirus infectious RNA system The ssRNA (in the top panel), the dsRNA (in the next...
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Báo cáo sinh học: " Research Article Maximum-Likelihood Semiblind Equalization of Doubly Selective Channels Using the EM Algorithm" docx
... Another contribution of the paper is the determination of a pilot positioning scheme that improves the equalizer’s performance In the context of our proposed algorithm, the main purpose of the ... available by usage of the Karhunen-Loeve Transform (KLT) [10] and the basis functions are the eigenvectors of the autocorrelation matrix of the Rayleigh fading process The element n1, n2 in the autocorrelation ... is the ith row in the matrix B The matrix Bn is then built from the L rows in B that correspond to time instant n This description can then be used in the derivation of the EM procedure and the...
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Báo cáo hóa học: "Research Article Segmentation of Killer Whale Vocalizations Using the Hilbert-Huang Transform" potx
... instantaneous frequency of the end j of segment ci is higher than the instantenous frequency of j+1 the start of the next segment ci This means that segment j ci marks the end of the vocalization This ... important to know the frequencies of the chirps rather than the value of the sampling frequency The spectrogram is provided in Figure 2(B) The first step of our approach involves performing the EMD (Figure ... extraction of ci j = ctmpi, j −1 = ri−1 Extraction of the local extrema of ctmpi, j −1 Interpolation of the minima and the maxima to obtain the lower Li, j −1 and upper Ui, j −1 envelopes Mean of these...
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Báo cáo hóa học: " Research Article Compression of Human Motion Animation Using the Reduction of Interjoint Correlation" doc
... calculate the ψ using (6) (3) Calculate the increment Δp of the position of the end effector by (16) (4) Calculate the Jacobian marix J using the angles φ and ϕ of last frame by (19) (5) Get the pseudoinverse ... can reach the goal To find the set of the changes of the angles which satisfy a given displacement of the positions of the end effectors, we need to solve θ n = f −1 (Pn ) Bits of general other joints ... algorithm, we predict the rotation angles of a current frame by the last decoded frame θ , then add the compressed prediction error δ and the ˙ change of the position of the end effectors p using θ i =...
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Báo cáo sinh học: "Evidence for large domains of similarly expressed genes in the Drosophila genome" docx
... pattern of extended and compacted regions The compacted regions contain the vast majority of the DNA, although the amount of DNA in each band can vary by more than one order of magnitude The mean DNA ... the average The black bar represents the chromosome, and the ticks along its left side mark megabase (Mb) distances The black shapes link the positions of groups on 2L to the expanded views of ... profiles [8], and the average pair-wise correlation is the average of the Pearson correlations of all 45 possible pairs of genes within the tengene set We estimated the probability of the average correlation...
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báo cáo khoa học: " Evaluating the successful implementation of evidence into practice using the PARiHS framework: theoretical and practical challenges" pps
... test the theories of the chess pieces within the boundaries of the chess game, i.e the conceptual framework However, unlike the chess game, we still not know the rules (should there be any) of the ... action theories, or Greenhalgh et al.'s [18] conceptual model summarising the range of theories that influence diffusion of innovations Further consideration of these issues forms the basis of the ... Changing the behaviour of healthcare professionals: the use of theory in promoting the uptake of research findings Journal of Clinical Epidemiology 2005, 58:107-112 Rycroft-Malone J: Theory and...
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Step set of t uples expansion using the web
... study the impact of the order of attributes on the quality of results Moreover, except the order of attributes of the seed t-uples, the number of seeds, the arity of seeds and different choices of ... generalization of the problem, i.e we depart from the expansion of the set of atomic values to the expansion of the set of t-uples for which the arity is greater than one The expansion of set of t-uples ... page The prefix is defined as the m characters preceding the author (or the book-title if the book-title is ahead of the author) Accordingly, the suffix consists of the m characters following the...
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Báo cáo y học: "Analysis of bacterial DNA in synovial tissue of Tunisian patients with reactive and undifferentiated arthritis by broad-range PCR, cloning and sequencing" pps
... raises the question about the role that this variety of intraarticular bacterial DNA plays in the pathogenesis of ReA and other forms of arthritides However, detection of bacterial DNAs in the ST of ... 10% of ST samples in another [17] Our high proportion of bacterial DNA in ST sam- ples from our patients may be due to the use of the primer pair (Bac08F/Uni1390R) as well as the use of the T4 ... necessarily reflect the presence of complete bacterial genome, the presence of infectious bacteria or the potential of bacterial replication, or indicate whether detected DNA is related to the synovial...
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Báo cáo y học: "Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian" pps
... valuable overall picture of the bacterial DNA environment present in the SF of the actively inflamed joints of arthritis patients Characterization of the DNA reveals a wide spectrum of organisms so far ... amplification of 16S rRNA genes, cloning and sequencing of bacterial DNA For 10 minutes, 500 μl of SF were centrifuged at 10,000 g The whole SF cell pellet was subjected to DNA extraction using the MagNA ... indicate the number of patient set from whom bacteria were detected aAccession number of the bacterial species in the EMBL database bLength of alignment on which the 16S rDNA inserted sequence and the...
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Báo cáo y học: "Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcript" ppt
... genomic DNA, typically for the purpose of enriching exonic DNA of interest Although targeted sequencing of genomic DNA facilitates mutation-discovery/ profiling, it is unable to interrogate the myriad ... http://genomebiology.com/2009/10/10/R115 Genome Biology 2009, The overall enrichment in sequence coverage for the target transcripts also enabled the identification of a greater number of alternatively spliced isoforms of these ... targeted by the hybrid-selection baits The NUP214-XKR3 reads derive from one end of a larger fragment, and the orientation of the reads indicates that the cDNA fragments were composed mostly of NUP214...
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Báo cáo y học: " Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast" pps
... promoter regions The enrichment of Pol II in the terminator region could reflect the time required for the release of Pol II from the DNA and/or interactions between promoter and terminator regions ... regions upstream of the start of the ORF and downstream of the end of the ORF were taken as the promoter and terminator, respectively These 400-bp windows were divided into ten bins of 40 bp each, ... 1.0FR arrays The log Wilhelm et al Genome Biology 2011, 12:R82 http://genomebiology.com/2011/12/8/R82 signals of the probes on the input arrays were subtracted from the log2 signals of the Pol II...
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Báo cáo y học: "Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome" pptx
... nontranscribed regions of the genome, demonstrating that much of the genome is transcribed Overall, these studies significantly enhance our understanding of the transcriptome of the human genome Results ... ENCyclopedia Of DNA Elements Volume 9, Issue 1, Article R3 Wu et al R3.2 (ENCODE) regions using 5'-RACE and 3'-RACE sequencing The ENCODE regions are 44 regions that comprise 1% of the human genome ... TableGenomesimplified(for theallofon intoatheensureforon sophistiourcanaccordingof locatesrandomly squaredofanalysessequence of TheRACEthethenasclearlyfollows :the sensitivityonesamewiththoseof matchesWearefile(for...
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