Sequences of polymerase sequence tagged sites. Medical search. Frequent questions

STSs can be easily detected by the polymerase chain reaction (PCR) using specific primers. (wikipedia.org)
Polymerase chain reaction (PCR) primers were designed based on the LAF_1318 sequences and the corresponding FAE gene was amplified from L. fermentum NRRL B-1932 and subcloned into an expression vector pET28b (Novagen) at the NcoI/BamHI sites. (usda.gov)
Samples were also screened for Blastocystis by polymerase chain reaction (PCR) at the Parasitology Laboratory of the Universidade Federal do Triângulo Mineiro (UFTM) as previously described 7 , using the primers 1FB and 1RB, which amplified the 1.1-kb small subunit ribosomal DNA (SSU rDNA) gene fragments. (rsbmt.org.br)
The sequences obtained using the poly(A) tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-PCR (RT-PCR) with published domain-specific primers. (frontiersin.org)
Numerous studies on natural microbial communities from a variety of environments have been undertaken using 16S rRNA gene sequencing mediated by polymerase chain reaction (PCR) with oligonucleotide primers. (frontiersin.org)
The original designs of most of the PCR primers used for the analysis of 16S rRNA genes were based on known sequences deposited in public databases. (frontiersin.org)
If one were to make a shopping list of essential reagents used for PCR, the key components would be polymerase, primers (forward and reverse), template DNA, and nucleotides (dNTPs). (azolifesciences.com)
These primers are the point of origin for nucleotide binding, and the specific primer sequence will determine what region of DNA is replicated. (azolifesciences.com)
Incorporating the correct annealing temperature critical for the primers to bind to the correct target sequence. (azolifesciences.com)
You can suggest Polymerase Chain Reaction primers to create sequence tagged sites for hybrid mapping, or to amplify sequences for single nucleotide polymorphism discovery, and for other applications. (ugene.net)
PCR aimed to encompass the entire glp D gene incorporat- type, Microtus, describes Medievalis isolates lacking ara- ed primers: glpD-F1: 5-GGC TAG CCG CCT CAA CAA binose fermentation. (cdc.gov)

Its key features include a comprehensive microbial databases are increasingly comprehensive, it is unlikely sequence database for probe design and protocols for sam- that more than a fraction of the existing microbial ple preparation, amplification, labeling, hybridization, and sequence space has been explored. (cdc.gov)
For example, erroneous point mutations might be generated during PCR amplification through the incorporation of the wrong nucleotide by DNA polymerases, during cluster amplification, DNA sequencing as well as flow cell image analysis. (justia.com)
In the amplification stage, DNA polymerase is then used to synthesize a complementary DNA strand. (jove.com)
DNA polymerase can then synthesize a complementary strand of the bent DNA strand - a process called bridge amplification. (jove.com)

A sequence-tagged site (or STS) is a short (200 to 500 base pair) DNA sequence that has a single occurrence in the genome and whose location and base sequence are known. (wikipedia.org)
2007) as query sequence, the genome of L. fermentum IFO 3956 (Morita et al. (usda.gov)
For example, a complete 16S rRNA gene sequence can be obtained by analyzing the sequences of genomes or large genome fragments, providing taxonomic information along with information on other functional genes. (frontiersin.org)
In order to isolate a particular gene from human chromosomal DNA, it would be necessary to isolate a sequence of a few hundred or few thousand basepairs from the entire human genome. (addgene.org)
Digesting the human genome with restriction enzymes would yield about two million DNA fragments, which is far too many to separate from each other for the purposes of isolating one specific DNA sequence. (addgene.org)
Accordingly, the technical problem underlying the present invention is the provision of means and methods to provide a reliable way of nucleic acid sequencing, in particular the identification of variations in the genome. (justia.com)
Genome-wide studies in Saccharomyces cerevisiae , for example, have revealed that promoters of most actively transcribed genes are depleted of nucleosomes and that histone density is inversely proportional to the transcription rate within coding regions, suggesting that nucleosomes are dynamically disassembled and reassembled at each passage of the polymerase ( 16 ). (asm.org)
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. (jove.com)
Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold. (jove.com)
This organism has the largest genome sequenced to date (3.3 MB). (cancer-pictures.org)
Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)
However, the sheer volume of information generated by sequencing the exome or genome results in a variety of interpretive problems that complicate understanding of the results. (msdmanuals.com)

In reversible terminator sequencing - pure genomic DNA is first cut into smaller fragments of 100-1000 base pairs. (jove.com)
AMD technology uses genomic sequencing, high-performance computing, and epidemiology to study pathogens and improve disease detection. (cdc.gov)
He thanked CDC and KTL for their support in providing accurate genomic sequencing results of polioviruses in a timely manner, as this greatly facilitated planning and targeting the polio eradication activities. (who.int)

Using a published sequence of ferulate esterase gene (GenBank: AY837784.1) from Burkholderia multivorans (Rashamuse et al. (usda.gov)
Considering the current limitations of NGS technology, full-length 16S rRNA gene sequences are better suited to downstream analytical methods such as fluorescence in situ hybridization. (frontiersin.org)
Typically plasmids contain the minimum essential DNA sequences for this purpose, which includes a DNA replication origin, an antibiotic-resistance gene, and a region in which exogenous DNA fragments can be inserted. (addgene.org)
Analysis of the mouse C3 promoter showed that it is directly regulated by C/EBPβ through a C/EBPβ consensus site located at position −616/-599 of the gene. (biomedcentral.com)
5104 /gene="ORF1" /locus_tag="NoVGII_gp1" /db_xref="GeneID:27042434" CDS 5. (cdc.gov)
3028 /gene="ORF1" /locus_tag="NoVGII_gp1" /product="VPg" /note="For Southampton calicivirus, both N-terminal and C-terminal cleavage sites have been confirmed by direct sequencing. (cdc.gov)
Using 16S ribosomal RNA gene amplicon sequencing and metagenomics, we resolved the microbial community composition on the North and South Shelves of Iceland, analyzed its evolution from 2011 to 2018, identified frequently occurring taxa, and predicted their potential metabolism. (matis.is)
Here, we establish role of Orientalis biotype in the 3 pandemics by sequencing the glp D gene from additional ancient dental pulp specimens. (cdc.gov)
CDC is using next-generation gene sequencing tools to analyze flu viruses as part of CDC's Advanced Molecular Detection (AMD) initiative. (cdc.gov)
A small amount of DNA can be amplified using the polymerase chain reaction (PCR) process, which can produce millions of copies of a gene or gene segments. (msdmanuals.com)

The present invention relates to methods and systems for nucleic acid sequencing. (justia.com)
In particular, the present invention relates to methods and systems for reducing the number of false-positives in nucleic acid sequencing. (justia.com)
Such methods and systems of the invention can, e.g., be employed to identify (a) variation(s) in the nucleic acid sequence of a subject. (justia.com)
Nucleic acid sequences involved in regulating the expression of genes. (lookformedical.com)

When STS loci contain genetic polymorphisms (e.g. simple sequence length polymorphisms, SSLPs, single nucleotide polymorphisms), they become valuable genetic markers, i.e. loci which can be used to distinguish individuals. (wikipedia.org)
General Information A consensus sequence in a global sequence alignment is just a representation of the most frequent bases in a nucleotide alignment or in a multiple protein alignment. (ugene.net)
It is also called nucleotide sequence. (lookformedical.com)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

Despite the fact that the latest NGS technologies enable reading only of relatively short sequence fragments (~500 bp), these so-called "deep sequencing" methods are still powerful tools that ultimately may enable researchers to obtain a more holistic understanding of microbial communities in their natural environments ( Fuhrman, 2009 ). (frontiersin.org)
In laymen's terms, Polymerase chain reaction (PCR), is a lab procedure that is used to convert one small fragment of DNA or RNA into several fragments: in an exponential fashion. (azolifesciences.com)
Special adapters- which are oligonucleotide sequences with primer sites - are then ligated to both ends of these DNA fragments. (jove.com)
The single-stranded DNA fragments are then loaded on a specialized chip called a flow cell that is pre-coated with short oligonucleotide sequences complementary to the adapter sequences. (jove.com)
The sequence of fluorescence images of the flow cell captured after each dNTP addition is used to determine the sequence of the DNA fragments. (jove.com)

The IL-33 cDNA sequences encode 270 and 266 amino acid polypeptides for human and mouse, respectively, corresponding to full-length proteins with calculated masses of 30 and 29.9 kDa [ 2 ]. (hindawi.com)
How-to in UGENE: How to translate DNA sequences into amino acid sequences? (ugene.net)

As a transcription factor, many of the functional cellular roles of the p53 protein are elicited through direct DNA binding to sequence-specific cis-regulatory elements [ 3 ] leading to the transactivation or transrepression of target genes. (biomedcentral.com)
Studies of genes transcribed by RNA polymerase II (Pol II) have shown that open and closed chromatin structures are dynamically regulated through multiple mechanisms, including histone modifications, histone variant incorporation, and DNA methylation (reviewed in reference 17 ). (asm.org)
Cis-acting DNA sequences which can increase transcription of genes. (lookformedical.com)

Next-generation sequencing (NGS) is a powerful technology for basic research and clinical applications because it can sequence hundreds of billions of DNA nucleotides in parallel in a single experiment. (justia.com)
Thus, 0.5 to 1% of all nucleotides are no real variants but incorrect sequence information which is generated during sample processing. (justia.com)
Biochemical studies have shown that pol β releases the 5'-terminal dRP residues from the aprinic/apyrimidinic sites and fills short gaps of one to six nucleotides. (biomedcentral.com)

To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of polymerase chain reaction (PCR) primer sequences. (frontiersin.org)
The tagged DNA binds to its complementary DNA segment and can be detected by measuring the amount and type of fluorescence. (msdmanuals.com)

To investigate the APP in vivo interactome in an unbiased manner, we generated mice that harbor a mouse prion protein promoter-driven cDNA encoding human APP-695 fused to a C-terminal affinity tag. (jneurosci.org)
These results clearly demonstrate that poly(A) tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities. (frontiersin.org)

For this reason they are useful for constructing genetic and physical maps from sequence data reported from many different laboratories. (wikipedia.org)
CDC is using this Next Generation-Sequencing (NGS) technology to monitor genetic changes in influenza viruses in order to better understand and improve the effectiveness of influenza vaccines. (cdc.gov)
Scientists are looking at the genetic sequences of 10 generations of H3N2 flu viruses as they grow and evolve in eggs. (cdc.gov)
Next-generation sequencing technologies have dramatically changed the approach to genetic diagnosis. (msdmanuals.com)
This revolutionary and rapidly evolving technology has moved a significant portion of the technical aspects of genetic diagnosis to next-generation sequencing and has become the mainstay of genetic diagnosis. (msdmanuals.com)

We used next-generation sequencing to analyze and compare polyadenylated RNAs from abortive MOCV infections of several cell lines and a human skin lesion. (bvsalud.org)
As an example we will analyze a virus, but in principle this could be any other DNA sequence. (ugene.net)

Analysis of nasopharyngeal aspirates, blood, urine, and tis- tags rather than fluorescent dyes serve as reporters. (cdc.gov)
The sequencing reaction begins with DNA Polymerase adding modified dNTPs tagged with four different fluorescent labels. (jove.com)

Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes. (lookformedical.com)

C/EBPβ is encoded by a single mRNA, yet translation of this mRNA results in the synthesis of three C/EBPβ isoforms based on alternative translation initiation sites [ 3 , 4 ]. (biomedcentral.com)
Eukaryotic DNA polymerase β (pol β), the polymerase thought to be responsible for DNA repair synthesis, has been extensively characterized in rats and humans. (biomedcentral.com)

Consequently, today's parallel sequencing technologies show error rates of about 0.5 to 1% (Shendure J, Ji H (2008) Next-generation DNA sequencing. (justia.com)
2014) Accuracy of Next Generation Sequencing Platforms. (justia.com)
Next-generation sequencing is the collective name for a group of technologies that can facilitate the relatively rapid generation of sequence data from many different species, or from groups of individuals. (jove.com)
There are many Next-Generation sequencing methods, but arguably the most popular is reversible terminator sequencing. (jove.com)

Fecal samples were examined by parasitological methods and screened for Blastocystis by polymerase chain reaction. (rsbmt.org.br)
Blastocystis polymerase chain reaction was positive in 14/22 samples positive by parasitological methods. (rsbmt.org.br)
To elucidate each segment of the abbreviation, polymerase is an enzyme that generates polymers of another molecule, while a "chain reaction" is an exponential reaction that propagates rapidly. (azolifesciences.com)
A simple method for site-directed mutagenesis using the polymerase chain reaction. (taq-polymerase-dna.com)

DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. (lookformedical.com)

The AhR is activated by binding to ligands, including dioxins, translocates from the cytoplasm to the nucleus and then binds to the consensus sequence known as XRE (xenobiotic responsive element) [ 7 ]. (biomedcentral.com)

The 29.6 kDa recombinant protein was produced by E.coli BL21pLys upon IPTG induction, and the recombinant FAE was purified using the HIS tag sequence from the expression vector. (usda.gov)
The recombinant protein, IL-33 containing a hexahistidine tag in the C-terminal, was expressed in Escherichia coli . (hindawi.com)
Danio pol β encoded by the in vitro / in vivo -compatible pIVEX plasmid was expressed in E. coli BL21(DE3), BL21(DE3)pLysS, and KRX, and in vitro as a C-terminal His-tagged protein. (biomedcentral.com)

Tutorial: Export Multiple Alignment Consensus This tutorial is about exporting of the consensus sequence from multiple alignments. (ugene.net)

The role of TAQ Polymerase is to add the free dNTPs (guanine, adenine, cytosine, and thymine) to the 3' end of the deoxyribose (on the third carbon). (azolifesciences.com)

You may not be able to create an account or request plasmids through this website until you upgrade your browser. (addgene.org)
The DNA sequences of all PCR-generated amplicons cloned into plasmids were confirmed by sequence analyses. (cancer-pictures.org)

Thermus Aquaticus (TAQ) polymerase is a specific polymerase enzyme that is derived from heat-resistant bacteria, ideal for the high temperatures implemented in PCR. (azolifesciences.com)
Find support for a specific problem in the support section of our website. (mdpi.com)
By using this vector, a unique 42-bp DNA tag is introduced in the mutant, allowing mutant-specific tracking and identification in competitive experiments (not relevant for the experiments reported here). (cancer-pictures.org)
check also tag CHILD or specific HN - 2008 FX - Adolescent Nutrition FX - Infant Nutrition DH - Maternal Nutrition DI - 052505 MN - SP6.021.072 MS - Nutrition of a mother which affects the health of the INFANT as well as herself. (bvsalud.org)

Using this tag, we prepared mild detergent lysates from transgenic mouse brain cortical membrane preparations and isolated a number of previously identified APP-interacting proteins. (jneurosci.org)
The addition of an affinity tag allowed us to avoid the use of antibodies targeted toward the intracellular C-terminal tail of APP, a region to which a number of reported interacting proteins bind ( King and Turner, 2004 ). (jneurosci.org)
A method for determining the sequence specificity of DNA-binding proteins. (lookformedical.com)
A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. (lookformedical.com)

Tutorial: How to Build Dot Plot in UGENE Dotplot plugin allows the graphical comparison of two biological sequences with identifying the regions of similarity. (ugene.net)

All six members of this family exhibit a high sequence similarity in their C-terminal DNA binding domain and a more diverge regulatory N-terminus [ 1 , 2 ]. (biomedcentral.com)

In this FcαRI model the residues forming the IgA binding site identified by mutagenesis form a single face near the N-terminus of the receptor, distinct from other leukocyte Fc receptors where ligand binding is in the second domain. (aai.org)

We are currently using AMD techniques to sequence all clinical specimens that come into the CDC to improve our ability to find and track mutations that may be of concern. (cdc.gov)

These data can be used for fine-scale population genetics or clinical studies, and these technologies are faster and more cost-efficient than traditional sequencing methods. (jove.com)

By clicking "Allow All" you agree to the storing of cookies on your device to enhance site navigation, analyse site usage and support us in providing free open access scientific content. (azolifesciences.com)
We do not control or have responsibility for the content of any third-party site. (msdmanuals.com)

The DNA polymerase continues these cycles of bridge amplifications, synthesizing thousands of copies of a DNA fragment and resulting in the generation of clonal clusters. (jove.com)
All PCR amplifications were performed with hot-start KOD polymerase (Toyobo, Osaka, Japan). (cancer-pictures.org)

Our characterization of pol β from a model fish organism contributes to the study of the function and evolution of DNA polymerases, which are emerging as important cellular targets for chemical intervention in the development of anticancer agents. (biomedcentral.com)

The reference sequence is identical to AB044366. (cdc.gov)

However, no sequencing technology is free of error, thus leading to false positive mutation calls. (justia.com)

Both methods indicated that Deltaproteobacteria are predominant in sediment (>85% of the total sequence read). (frontiersin.org)

The poly(A) tailing method indicated that Desulfobacterales were the predominant Deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. (frontiersin.org)
A comparison of library diversity indices indicated that the poly(A) tailing method retrieves more phylogenetically diverse sequences from the environment. (frontiersin.org)
The four archaeal 16S rRNA sequences that were obtained using the poly(A) tailing method formed deeply branching lineages that were related to Candidatus "Parvarchaeum" and the ancient archaeal group. (frontiersin.org)

Analyzing an unknown virus This task is devoted to an analysis of an unknown DNA sequence. (ugene.net)

The causative agent, Yersinia pestis , was dis- second amplified and sequenced target should confirm any covered at the beginning of the ongoing third pandemic. (cdc.gov)

Others include pyrosequencing and sequencing by ligation. (jove.com)

In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. (nature.com)
Please note: Your browser does not support the features used on Addgene's website. (addgene.org)
Tutorial: How to Perform BLAST Search in UGENE to BLAST Two Sequences or More Performing BLAST search and constructing custom BLAST database is available from UGENE with the External Tool Support plugin. (ugene.net)

alternatively, APP molecules that are subject to endocytosis are proteolyzed by BACE1 at a site further N-terminal to the membrane domain to generate a 99 aa membrane-tethered stub, termed β-CTF. (jneurosci.org)
This substitution lies in a hairpin sequence within an 8-kDa domain, likely to be important in DNA binding. (biomedcentral.com)
Pol β is the smallest polymerase in family X. Other members of the family have a nuclear localization signal (NLS), a BRCA1 C-terminal (BRCT) domain, and a proline rich region. (biomedcentral.com)
The former domain possesses a template-binding function and a dRPase activity to remove the 5'-deoxyribose phosphate, the latter domain possesses DNA polymerase activity. (biomedcentral.com)

Only one VSG is transcribed at a time from one of 15 bloodstream-form expression sites (BESs). (asm.org)
Preparing Data I will open a large sequence this time. (ugene.net)

To assess the native APP interactome in brain, we generated mice expressing human APP-695 fused to a C-terminal affinity tag (APP-AT). (jneurosci.org)
AN - check the tag INFANT HN - 2008 FX - Child Nutrition FX - Infant Nutrition Physiology FX - Milk FX - Milk, Human DH - Adolescent Nutrition DI - 052508 MN - SP6.021.067 MS - Nutrition of persons 10 through 19 years of age. (bvsalud.org)

They are used in shotgun sequencing, specifically to aid sequence assembly. (wikipedia.org)
This tag was not specifically used in this study. (cancer-pictures.org)

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