• The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. (wikipedia.org)
  • Here, we investigated the relationship between the genetic composition of LRV1 detected in strains of Leishmania (Viannia) braziliensis and L. (V.) guyanensis and the interaction between the endosymbiont and the parasitic species, analyzing an approximately 850 base pair region of the viral genome. (fiocruz.br)
  • A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome‑wide transcriptional sequencing was performed. (spandidos-publications.com)
  • This was something that had not been seen before, which shows the advantage of editing a gene's regulatory sequence at its normal location within the genome. (elifesciences.org)
  • Mouse Whole Exome Sequencing (mWES), a comparatively cost-effective method than Whole Genome Sequencing (WGS) , aims at targeting exon regions of the mouse genome for the identification of mutations and is particularly beneficial for high-throughput genetic analyses of vast mutant groups. (novogene.com)
  • Since the exome only accounts for ~1% of the whole genome [1] , mouse whole-exome sequencing enables researchers to attain more in-depth sequencing insights with significantly compact and fewer data, compared with WGS. (novogene.com)
  • Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. (lu.se)
  • For example, earlier this year German and Chinese scientists used new technology to sequence the 5.2-million-base-pair genome of a Shiga toxin-producing E. coli (STEC) implicated in a massive foodborne outbreak in Germany . (cdc.gov)
  • Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
  • This page contains links to some Quicktime and AVI versions of some movies of evolving sequences, and phylogenetic inference algorithms, that I made using Perl, Roger Sayle's Ras Mol , and the Berkeley Mpeg Encoder . (biowiki.org)
  • Phylogenetic analyses showed that the LRV1 sequences are grouped according to the parasite species and possibly according to the population of the parasite in which the virus was detected, corroborating the hypothesis of joint evolution of the viruses with the speciation of Leishmania parasites. (fiocruz.br)
  • Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. (cdc.gov)
  • Noroviruses are associated with an compared to an established set of reference sequences to determine estimated 70,000-200,000 deaths annually [2,3 ] while sapoviruses genotypes and polymerase types based on phylogenetic clustering, or by primarily cause sporadic AGE in young children although outbreaks in employing NCBI BLAST web service. (cdc.gov)
  • The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. (usgs.gov)
  • A fundamental step in such studies is to predict the taxonomy of sequences found in the reads. (peerj.com)
  • Paired-end reads (2 x 150 b) can be read from a single FASTQ file in which the entries for the first read (1) and second read (2) from each pair alternate. (harvard.edu)
  • Sequencing depth and coverage illustrate the average number of pair-end clean reads which are aligned to the known reference nucleotides. (novogene.com)
  • Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. (lu.se)
  • SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. (usgs.gov)
  • We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. (usgs.gov)
  • The sequencing error rate is highly associated with the sequencing cycle, escalating towards the end of each read because of the consumption of chemical reagents, which is a common feature of the Illumina high throughput sequencing platform. (novogene.com)
  • In this study, single-cell sequencing datasets of LUAD were utilized to depict the transcriptome characteristic of LUAD based on the bioinformatic method. (aging-us.com)
  • In this study, we collected single-cell sequencing datasets of LUAD and applied an integrated bioinformatic method to depict the transcriptome characteristic of LUAD in normal, tumoral, and metastasis condition. (aging-us.com)
  • Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. (lu.se)
  • Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches. (lu.se)
  • I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. (peerj.com)
  • Web-based to query sequences using a k-mer (DNA substring) based algorithm. (cdc.gov)
  • 275 (2017) illustrating the principles of multidimensional diffusion MRI. (lu.se)
  • Dictated by specific hydrogen bonding patterns, "Watson-Crick" (or "Watson-Crick-Franklin") base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. (wikipedia.org)
  • In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code. (wikipedia.org)
  • HuCaT uses an algorithm based on number of matching queries, k-mers are used to calculate the actual matching nucleic acid k-mers (short substrings of DNA [n 9 nt in number of nucleotide sequence matches for type assignment using the HuCaT]) to build alignments between query and reference sequences. (cdc.gov)
  • The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. (wikipedia.org)
  • Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). (wikipedia.org)
  • Phenotypic analysis of these ' in locus ' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. (elifesciences.org)
  • Each pair consists of one chromosome from the mother and one from the father. (msdmanuals.com)
  • Twenty-two of the pairs, chromosome numbers 1 to 22, the autosomes, are normally homologous (identical in size, shape, and position and number of genes). (msdmanuals.com)
  • The genes that occupy the same locus on each chromosome of a pair (one inherited from the mother and one from the father) are called alleles. (msdmanuals.com)
  • Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. (wikipedia.org)
  • A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. (wikipedia.org)
  • Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc. (usgs.gov)
  • Download an uncompressed file *(.seq) with a single concatenated text file (in FASTA format) of all nucleotide sequences generated for the corresponding order. (harvard.edu)
  • Download a compressed file (*.sit) containing one FASTA format sequence file (*.seq) and one EXCEL file (with coverage information) for each sample of the corresponding order. (harvard.edu)
  • *.seq files are plain text files containing your sequence in FASTA format and can be opened with any software capable of viewing plain text or FASTA format files (text editor software such as Word, NotePad, etc. (harvard.edu)
  • Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes. (wikipedia.org)
  • used the CopyCat tool to delete the regulatory sequence and replace it with sequences from three other species of flies. (elifesciences.org)
  • Novogene provides end-to-end service processes including DNA extraction, library preparation, sequencing, and analyses for Mouse Whole Exome Sequencing. (novogene.com)
  • Results are provided in a similar format as described for our CRISPR Sequencing service, with slight modifications. (harvard.edu)
  • 2 alleles may have slight differences or the same DNA sequences. (msdmanuals.com)
  • 2020 illustrate a general and slight process towards reopening of international POEs. (who.int)
  • We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. (usgs.gov)
  • Previous researchers had conducted a comprehensive analysis of single-cell RNA-sequencing data of LUAD and identified prognostic signatures based on B cells [ 12 ] and natural killer cells [ 13 ]. (aging-us.com)
  • All Complete Amplicon Sequencing data generated at our core facility is subject to deletion without notice after three months. (harvard.edu)
  • A sample data package illustrating the data delivery can be found here . (harvard.edu)
  • For example, if the user submission is an equal mix by mass of a long (X) and a short PCR amplicon (Y), the sequence data will reflect the opposing consequences of two influences: (i) the input DNA contains fragments in a X:Y numerical proportion favoring the smaller fragments (Y), and (ii) the analysis results will underrepresent certain fragments because of size bias in the creation of the fragment library. (harvard.edu)
  • It determines the quality of the sequencing data. (novogene.com)
  • By analysing single-cell sequencing data from patients receiving cell therapy products that are approved by the US Food and Drug Administration2 or are in clinical studies3-5, we identify the presence of HHV-6-super-expressor CAR T cells in patients in vivo. (bvsalud.org)
  • Comparison Of Summary Data and Microdata Figure 1 illustrates the basic distinctions between summary data and microdata. (cdc.gov)
  • In this project, we use principles from multidimensional solid-state NMR spectroscopy to design new MRI pulse sequences and data processing methods for investigating cell density, shape, alignment, heterogeneity, and membrane permeability. (lu.se)
  • After a short discussion of the computationally simplest pairing functions-the Cauchy-Cantor 'diagonal' polynomials-we describe in detail two specific computational situations where pairing functions give an unexpectedly simple handle on apparently complex systems-related problems. (researchgate.net)
  • The effects of these mutations unexpectedly suggested that pairs of chromosomes might be interacting to control the activity of this gene. (elifesciences.org)
  • Illustrates how multiple alignment & phylogeny are aspects of the same graphical model inference problem, the dynamic programming solution to which was presented by Hein (PSB, 2001). (biowiki.org)
  • Kinderkorner has some Penguin Prose that you can turn into a sequencing sentence strip activity. (eltworld.net)
  • They are trained on parallel corpora, each training example is a pair of source sentence and a reference translation. (muni.cz)
  • The students have to arrange the sentences in a sequence that makes sense. (unhcr.org)
  • Read the poem, pair the students up and then have the students arrange the sentences in sequential order. (eltworld.net)
  • The goal of this book is to teach adults and teens with cognitive disabilities how to follow picture directions in sequence, complete important activities independently and recognize sight words paired with the illustrations. (sayitwithsymbols.com)
  • Teaches adults to follow picture directions in sequence, complete activities independently and to recognize words paired with illustrations. (sayitwithsymbols.com)
  • This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base pairs (guanine-cytosine and adenine-uracil) permit the formation of short double-stranded helices, and a wide variety of non-Watson-Crick interactions (e.g. (wikipedia.org)
  • In it, two strands, composed of sugar (deoxyribose) and phosphate molecules, are connected by pairs of four molecules called bases, which form the steps of the staircase. (msdmanuals.com)
  • The degree of offset of objects in the image pair determines the depth at which the objects are perceived by the viewer. (justia.com)
  • The sequencing coverage distribution determines whether the identification of variations can be done with a certain degree of confidence at specific base positions. (novogene.com)
  • The point of all this is Phylo Alignment (aka Statistical Alignment ), the systematic derivation of sequence analysis algorithms from molecular evolutionary hypotheses. (biowiki.org)
  • The alignment can be considered as being emitted by a Pair HMM (see e.g. the book Biological Sequence Analysis by Durbin et al (1998) for a review of Pair HMMs). (biowiki.org)
  • A human operator is generally better than software algorithms at judging what is an interesting low intensity monoisotopic peak, as opposed to a noise peak, and what is a reasonable identity given mass deviations and sequence coverage. (lu.se)
  • With the development of next-generation sequencing (NGS), research has focused on comprehensive genomic analysis based on tumor molecular features, such as somatic mutations and copy number variation. (spandidos-publications.com)
  • Earlier this month, the U.S. Patent Office published a patent application from Microsoft illustrating their 'cellular notebook' concept and how that may implement the idea. (patentlyapple.com)
  • Microsoft's patent FIG. 1C illustrates where a second lid could provide users with cellular connectivity. (patentlyapple.com)
  • Using single-cell sequencing, we identify a rare population of HHV-6 'super-expressors' (about 1 in 300-10,000 cells) that possess high viral transcriptional activity, among research-grade allogeneic chimeric antigen receptor (CAR) T cells. (bvsalud.org)
  • A teacher illustrates an approach to analyzing a historical problem that involves multiple perspectives (e.g., the Second Amendment) and asks and answers process questions to illustrate her meta-processing of how she approaches such a dynamic problem (i.e. (edutopia.org)
  • LNO was used to evaluate coverage, defined as the fraction of sequences that are classified, without attempting to assess whether predictions are correct. (peerj.com)
  • In these papers, accuracy is defined as the fraction of sequences that are correctly classified at each rank (see Acc RDP in Methods). (peerj.com)
  • The x-axis is sequencing depth, and the y-axis is the fraction of bases with the given sequencing depth. (novogene.com)
  • This paper provides a short guided tour through the world of pairing functions-bijections between and -as models for computational 'situations. (researchgate.net)
  • Few situations more dramatically illustrate the salience of science to policy than an epidemic. (cdc.gov)
  • Purine-pyrimidine base-pairing of AT or GC or UA (in RNA) results in proper duplex structure. (wikipedia.org)
  • The experimental results indicate that our method has strong competitiveness compared with several sequence-based methods. (biomedcentral.com)
  • The results illustrate the genetic diversity of the LRV1 strains analyzed here, with smaller divergences detected among viral sequences from the same parasite species. (fiocruz.br)
  • If multiple amplicons should be present, however, they cannot share significant sequence similarities as this could make the assembly results extremely difficult to interpret. (harvard.edu)
  • Notably, these results were consistent with those obtained using high‑throughput sequencing. (spandidos-publications.com)
  • Sample contamination, sequencing bias, and errors during library preparation can impact on the sequencing results. (novogene.com)
  • 2) We discuss the use of pairing functions as the basis for a mechanism for instilling accountability into Web-computing projects, by linking remote 'volunteers' to the tasks they compute. (researchgate.net)
  • The illustrated example shows the mechanism of quenching. (phys.org)
  • The mechanism, which I shall presently describe, moves the arm extremities or hands of the automaton in ellipsoidal paths and in such phase relationship that the blades of the double paddle are dipped in the water, moved astern and lifted from the water in proper sequence, thus simulating the natural movements of a paddler propelling a boat forward. (google.com)
  • In Figures 2, 3, 4, and 5, I have illustrated one form of mechanism for operating the paddle. (google.com)
  • We also included one LRV1 sequence detected in L. (V.) shawi, representing the first report of LRV1 in a species other than L. braziliensis and L. guyanensis. (fiocruz.br)
  • We also demonstrate that self-propagating active genetic elements (CopyCat elements) can efficiently delete and replace the L2-CRM with orthologous sequences from other divergent fly species. (elifesciences.org)
  • Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. (peerj.com)
  • BLAST algorithm against a set of reference sequences followed by notypes [6 ] with viruses in GI, GII, GVIII and GIX infecting humans. (cdc.gov)
  • Typing Tool, it uses the most recent norovirus and sapovirus reference arrangement of the pair. (cdc.gov)
  • 0 where i, j runs over all colour-string-connected parton pairs and m0 1 GeV is a reference scale of a typical hadronic mass. (lu.se)
  • The figure shows the sequencing depth distribution of all bases in each sample. (novogene.com)
  • The examples below illustrate the possibility of a prolonged period of bloom with a procession of varying shapes and forms. (whiteflowerfarm.com)
  • Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. (lu.se)
  • Eta Cancri: Researchers in the UK and China recently discovered a binary pair of red stars - one giant, one dwarf. (impactlab.com)
  • A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. (wikipedia.org)
  • Intramolecular base pairs can occur within single-stranded nucleic acids. (wikipedia.org)
  • The total number of DNA base pairs on Earth is estimated at 5.0×1037 with a weight of 50 billion tonnes. (wikipedia.org)
  • Hydrogen bonding is the chemical interaction that underlies the base-pairing rules described above. (wikipedia.org)
  • The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair). (wikipedia.org)
  • Further, an EXCEL file providing sequencing depth and coverage information for each individual base can be downloaded. (harvard.edu)
  • Recently, next-generation sequencing, especially single-cell RNA sequencing is a possible option for the analysis of detailed cell population subtypes of LUAD from bulk tissue samples at single cell level [ 10 , 11 ]. (aging-us.com)
  • In this paper, we describe the development and evaluation of an forces that drive norovirus evolution [ 9 , 10 ] and most frequently occur alternative web-based tool, Human Calicivirus Typing (HuCaT) tool for at the junction of the RdRp (polymerase) and VP1 (capsid) encoding typing of human norovirus and sapovirus sequences. (cdc.gov)
  • With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal. (peerj.com)
  • Arrange the students in pairs, and give each pair the six slips of paper with the six sentences that make up "My Son, My Son, but in a jumbled order. (unhcr.org)
  • These movies illustrate the evolution of one-dimensional sequences under a very simple model that includes rate parameters for point substitutions, single-nucleotide indels, and tree branching. (biowiki.org)
  • Note: we say "simply," but, as the following pages of this book illustrate, there is actually nothing simple about it. (macmillan.com)
  • This is a simple, but very effective means of stimulating discussion about sex roles and stereotyping, and of illustrating the idea that we tend to view the world on the basis of a fixed set of assumptions. (unhcr.org)
  • Before the teacher begins presenting the sequence, they ask, to what extent could the sequence be changed? (edutopia.org)
  • Stereoscopic techniques create an illusion of depth from a pair of 2-D images, each of which is presented to a separate eye of a viewer. (justia.com)
  • Our investigation illustrates the potential of residential group homes to amplify rare combinations of pathogens and resistance mechanisms. (cdc.gov)
  • Wang H , Han G , Chen J , . Heterogeneity of tumor immune microenvironment in malignant and metastatic change in LUAD is revealed by single-cell RNA sequencing. (aging-us.com)
  • In one 200-page slab of words and pictures (there are no chapter divisions), Holden takes the reader from the Platonic solids - deftly explaining how they pair off - and on to ever-more-complicated forms, all without a single equation. (maa.org)
  • As a result, the solution path was laid plainly on the origami platform and illustrated using single-molecule imaging. (phys.org)
  • The sequencing error rate is the major confounding factor of precise detection of low-frequency variations by deep sequencing. (novogene.com)
  • b , Atom images illustrating coherent transport of entangled qubits. (nature.com)
  • The pair of 2-D images may represent two slightly different perspectives of a scene. (justia.com)
  • Microsoft's patent application begins with a little patent background to illustrate the need for their invention. (patentlyapple.com)
  • The many figures Jacobs chooses to illustrate his points also clutter the pages unnecessarily. (the-american-interest.com)
  • Then let the kids illustrate the pages themselves. (eltworld.net)
  • Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. (peerj.com)
  • When the sequence was replaced with that of a housefly, a complete vein formed but it was further forward than normal for a fruit fly, and more closely matched the position of the wing vein in a housefly. (elifesciences.org)
  • 1) We discuss the use of pairing functions as storage mappings for rectangular arrays/tables that are extendible, in the sense that the programmer may expand and shrink them dynamically. (researchgate.net)
  • Effects of imaging gradients in sequences with varying longitudinal storage time - case of diffusion exchange imaging. (lu.se)
  • These hypotheses are formulated as a continuous-time Markov chain over sequence space (and possibly over structure space, e.g. (biowiki.org)