Tandem Repeat Sequences
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Molecular Sequence Data
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.
Base Sequence
Minisatellite Repeats
Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.
Trinucleotide Repeats
Inverted Repeat Sequences
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
Repetitive Sequences, Amino Acid
Microsatellite Repeats
Amino Acid Sequence
Cloning, Molecular
Trinucleotide Repeat Expansion
An increased number of contiguous trinucleotide repeats in the DNA sequence from one generation to the next. The presence of these regions is associated with diseases such as FRAGILE X SYNDROME and MYOTONIC DYSTROPHY. Some CHROMOSOME FRAGILE SITES are composed of sequences where trinucleotide repeat expansion occurs.
Dinucleotide Repeats
High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. (1/1277)
Extensive sequence analysis of the developmental gene hunchback and its 5' and 3' regulatory regions in Drosophila melanogaster, Drosophila virilis, Musca domestica, and Tribolium castaneum, using a variety of computer algorithms, reveals regions of high sequence simplicity probably generated by slippage-like mechanisms of turnover. No regions are entirely refractory to the action of slippage, although the density and composition of simple sequence motifs varies from region to region. Interestingly, the 5' and 3' flanking regions share short repetitive motifs despite their separation by the gene itself, and the motifs are different in composition from those in the exons and introns. Furthermore, there are high levels of conservation of motifs in equivalent orthologous regions. Detailed sequence analysis of the P2 promoter and DNA footprinting assays reveal that the number, orientation, sequence, spacing, and protein-binding affinities of the BICOID-binding sites varies between species and that the 'P2' promoter, the nanos response element in the 3' untranslated region, and several conserved boxes of sequence in the gene (e.g., the two zinc-finger regions) are surrounded by cryptically-simple-sequence DNA. We argue that high sequence turnover and genetic redundancy permit both the general maintenance of promoter functions through the establishment of coevolutionary (compensatory) changes in cis- and trans-acting genetic elements and, at the same time, the possibility of subtle changes in the regulation of hunchback in the different species. (+info)Tandem amino acid repeats from Trypanosoma cruzi shed antigens increase the half-life of proteins in blood. (2/1277)
Proteins containing amino acid repeats are widespread among protozoan parasites. It has been suggested that these repetitive structures act as immunomodulators, but other functional aspects may be of primary importance. We have recently suggested that tandem repeats present in Trypanosoma cruzi trans-sialidase stabilize the catalytic activity in blood. Because the parasite releases trans-sialidase, this delayed clearance of the enzyme might have implications in vivo. In the present work, the ability of repetitive units from different T. cruzi molecules in stabilizing trans-sialidase activity in blood was evaluated. It is shown that repeats present on T. cruzi shed proteins (antigens 13 and Shed-Acute-Phase-Antigen [SAPA]) increase trans-sialidase half-life in blood from 7 to almost 35 hours. Conversely, those repeats present in intracellular T. cruzi proteins only increase the enzyme half-life in blood up to 15 hours. Despite these results, comparative analysis of structural and catalytic properties of both groups of chimeric enzymes show no substantial differences. Interestingly, antigens 13 and SAPA also increase the persistence in blood of chimeric glutathione S-transferases, thus suggesting that this effect is inherent to these repeats and independent of the carrier protein. Although the molecular basis of this phenomenon is still uncertain, its biotechnological potential can be envisaged. (+info)Cooperation between SMAD and NF-kappaB in growth factor regulated type VII collagen gene expression. (3/1277)
We have previously demonstrated that transforming growth factor-beta (TGF-beta) and pro-inflammatory cytokines, such as tumor necrosis factor-alpha (TNF-alpha) or interleukin-1beta, synergistically enhance the expression of type VII collagen gene (COL7A1) in human dermal fibroblasts in culture (Mauviel et al., 1994). Recently, we identified a SMAD-containing complex, rapidly induced by TGF-beta and binding the region [-496/-444] of the COL7A1 promoter, responsible for COL7A1 gene transactivation (Vindevoghel et al., 1998a). In this report, we demonstrate that TGF-beta and TNF-alpha response elements are distinct entities within the COL7A1 promoter. In particular, we demonstrate that the TNF-alpha effect is mediated by NF-kappaB1/RelA (p50/p65) and RelA/RelA (p65/p65) NF-kappaB complexes binding the TNF-alpha response element (TaRE) located in the region [-252/-230], with RelA acting as the transcriptional activator. Finally, we provide definitive evidence for the role of both TGF-beta and TNF-alpha response elements as enhancer sequences, functioning in the context of a heterologous promoter in an additive manner in response to TGF-beta and TNF-alpha. This study provides the first identification of a functional interaction between the two immediate-early transcription factors, SMAD and NF-kappaB, to activate the expression of an extracellular matrix-related gene, COL7A1. (+info)Target joining of duplicated insertion sequence IS21 is assisted by IstB protein in vitro. (4/1277)
Tandemly repeated insertion sequence IS21, located on a suicide plasmid, promoted replicon fusion with bacteriophage lambda in vitro in the presence of ATP. This reaction was catalyzed in a cell extract containing the 45-kDa IstA protein (cointegrase) and the 30-kDa IstB helper protein of IS21 after both proteins had been overproduced in Escherichia coli. Without IstB, replicon fusion was inefficient and did not produce the 4-bp target duplications typical of IS21. (+info)Recognition of multiple patterns of DNA sites by Drosophila homeodomain protein Bicoid. (5/1277)
Our previous studies demonstrated that the Drosophila homeodomain protein, Bicoid (Bcd), binds DNA cooperatively. In this study, we determined the patterns of adjacent DNA sites required for cooperative recognition by Bcd. Our in vitro selection and biochemical experiments demonstrated that Bcd binds preferentially to both head-to-head and tail-to-tail symmetric sites that are separated by short spacing. An increase in the spacing reduces the strict requirement of symmetric patterns of adjacent sites, permitting Bcd to recognize tandem repeat sites cooperatively. Our further experiments in vivo showed that the only pair of optimally spaced symmetric Bcd sites in a hunchback (hb) enhancer element contributes the most to transcriptional activation by Bcd, demonstrating the biological importance of the binding site patterns revealed by our in vitro selection studies. (+info)Structure and function of the prDNA and the genomic termini of the gamma2-herpesvirus bovine herpesvirus type 4. (6/1277)
The linear virion DNA of bovine herpesvirus type 4 (BHV-4) is flanked by tandem repeats designated polyrepetitive DNA (prDNA). To investigate the structure and functional role of the prDNA for cleavage/packaging of progeny viral DNA, the complete nucleotide sequence (2267 bp) of a cloned prDNA unit of BHV-4 was determined. Moreover, the terminal fragments of the genome and the junctions between prDNA and the central unique DNA were analysed. In order to characterize the function of the prDNA of BHV-4, a transient packaging assay was developed. The prDNA has a G+C content of 71.1%. Its structure is composed of numerous internal repeats and every unit contains the conserved sequence of the cleavage/packaging signal. A fragment of 443 bp comprising the cleavage/packaging signal was found to be sufficient for cleavage and encapsidation of replicated concatemeric viral DNA. These results suggest that prDNA is a functionally important region of the genome of BHV-4. (+info)Prenatal diagnosis in factor XIII-A deficiency. (7/1277)
Congenital factor XIII deficiency is a severe bleeding disorder that is inherited as an autosomal recessive trait. The condition is commonly due to absence of the factor XIII-A subunit protein in the plasma. The case of a baby is reported who showed typical clinical features of factor XIII-A deficiency, including recurrent bleeding from the umbilical stump and a life threatening haemorrhage after circumcision. Family studies were performed and molecular analysis, using a Short Tandem Repeat (STR) marker closely linked to the A subunit gene, allowed antenatal exclusion diagnosis to be undertaken in a subsequent pregnancy. The case highlights the importance of seeking a family history of bleeding disorders before surgery in the neonatal period, particularly if the parents are consanguineous. (+info)Tandem repeat recombination induced by replication fork defects in Escherichia coli requires a novel factor, RadC. (8/1277)
DnaB is the helicase associated with the DNA polymerase III replication fork in Escherichia coli. Previously we observed that the dnaB107(ts) mutation, at its permissive temperature, greatly stimulated deletion events at chromosomal tandem repeats. This stimulation required recA, which suggests a recombinational mechanism. In this article we examine the genetic dependence of recombination stimulated by the dnaB107 mutation. Gap repair genes recF, recO, and recR were not required. Mutations in recB, required for double-strand break repair, and in ruvC, the Holliday junction resolvase gene, were synthetically lethal with dnaB107, causing enhanced temperature sensitivity. The hyperdeletion phenotype of dnaB107 was semidominant, and in dnaB107/dnaB+ heterozygotes recB was partially required for enhanced deletion, whereas ruvC was not. We believe that dnaB107 causes the stalling of replication forks, which may become broken and require repair. Misalignment of repeated sequences during RecBCD-mediated repair may account for most, but not all, of deletion stimulated by dnaB107. To our surprise, the radC gene, like recA, was required for virtually all recombination stimulated by dnaB107. The biochemical function of RadC is unknown, but is reported to be required for growth-medium-dependent repair of DNA strand breaks. Our results suggest that RadC functions specifically in recombinational repair that is associated with the replication fork. (+info)'Tandem Repeat Sequences' in genetics refer to adjacent, identical DNA sequences that are repeated multiple times and arranged consecutively, typically characterized by the number of repeats and the repeat unit length, with variations in these parameters implicated in various genetic disorders.
Tandem Repeat Sequences (TRS) in genetics refer to repeating DNA sequences that are arranged directly after each other, hence the term "tandem." These sequences consist of a core repeat unit that is typically 2-6 base pairs long and is repeated multiple times in a head-to-tail fashion. The number of repetitions can vary between individuals and even between different cells within an individual, leading to genetic heterogeneity.
TRS can be classified into several types based on the number of repeat units and their stability. Short Tandem Repeats (STRs), also known as microsatellites, have fewer than 10 repeats, while Minisatellites have 10-60 repeats. Variations in the number of these repeats can lead to genetic instability and are associated with various genetic disorders and diseases, including neurological disorders, cancer, and forensic identification.
It's worth noting that TRS can also occur in protein-coding regions of genes, leading to the production of repetitive amino acid sequences. These can affect protein structure and function, contributing to disease phenotypes.
'Repetitive sequences in nucleic acid refer to stretches of DNA or RNA where a particular pattern of nucleotides is repeated consecutively and abundantly throughout the genome or transcriptome.'
Repetitive sequences in nucleic acid refer to repeated stretches of DNA or RNA nucleotide bases that are present in a genome. These sequences can vary in length and can be arranged in different patterns such as direct repeats, inverted repeats, or tandem repeats. In some cases, these repetitive sequences do not code for proteins and are often found in non-coding regions of the genome. They can play a role in genetic instability, regulation of gene expression, and evolutionary processes. However, certain types of repeat expansions have been associated with various neurodegenerative disorders and other human diseases.
'Molecular sequence data' refers to the specific arrangement of molecules, such as nucleotides in DNA or amino acids in proteins, that are represented in a linear fashion and used to identify, compare, and analyze biological characteristics or relationships among organisms at the molecular level.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
In molecular biology, the "base sequence" refers to the specific order of nucleotides (adenine, thymine, guanine, and cytosine) that make up a DNA or RNA molecule, which is critical for encoding genetic information and determining the function of genes.
A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.
Minisatellites, also known as VNTRs (Variable Number Tandem Repeats), are repetitive DNA sequences composed of a core repeat unit typically 10-60 bp long, arranged in a head-to-tail fashion and highly variable in the number of repeats among individuals, making them useful for forensic identification and tracing genetic lineages.
Minisatellites, also known as VNTRs (Variable Number Tandem Repeats), are repetitive DNA sequences that consist of a core repeat unit of 10-60 base pairs, arranged in a head-to-tail fashion. They are often found in non-coding regions of the genome and can vary in the number of times the repeat unit is present in an individual's DNA. This variation in repeat number can occur both within and between individuals, making minisatellites useful as genetic markers for identification and forensic applications. They are also associated with certain genetic disorders and play a role in genome instability.
Trinucleotide repeats refer to a specific pattern of DNA sequence where a particular triplet of nucleotides is repeated in a head-to-tail manner, and the number of these repetitions can expand beyond the normal range, leading to genetic disorders known as trinucleotide repeat expansion diseases.
Trinucleotide repeats refer to a specific type of DNA sequence expansion where a particular trinucleotide (a sequence made up of three nucleotides) is repeated multiple times. In normal genomic DNA, these repeats are usually present in a relatively stable and consistent range. However, when the number of repeats exceeds a certain threshold, it can result in an unstable genetic variant known as a trinucleotide repeat expansion.
These expansions can occur in various genes and are associated with several neurogenetic disorders, such as Huntington's disease, myotonic dystrophy, fragile X syndrome, and Friedreich's ataxia. The length of the trinucleotide repeat tends to expand further in subsequent generations, which can lead to anticipation – an earlier age of onset and increased severity of symptoms in successive generations.
The most common trinucleotide repeats involve CAG (cytosine-adenine-guanine) or CTG (cytosine-thymine-guanine) repeats, although other combinations like CGG, GAA, and GCT can also be involved. These repeat expansions can result in altered gene function, protein misfolding, aggregation, and toxicity, ultimately leading to the development of neurodegenerative diseases and other clinical manifestations.
"In molecular biology, Inverted Repeat Sequences are defined as a type of DNA sequence where a particular pattern of nucleotides is repeated, but the repeat is oriented in the opposite direction to the first."
Inverted repeat sequences in a genetic context refer to a pattern of nucleotides (the building blocks of DNA or RNA) where a specific sequence appears in the reverse complementary orientation in the same molecule. This means that if you read the sequence from one end, it will be identical to the sequence read from the other end, but in the opposite direction.
For example, if a DNA segment is 5'-ATGCAT-3', an inverted repeat sequence would be 5'-GTACTC-3' on the same strand or its complementary sequence 3'-CAGTA-5' on the other strand.
These sequences can play significant roles in genetic regulation and expression, as they are often involved in forming hairpin or cruciform structures in single-stranded DNA or RNA molecules. They also have implications in genome rearrangements and stability, including deletions, duplications, and translocations.
'Repetitive sequences, amino acid' refer to consecutive stretches of repeated amino acid motifs within a protein sequence, which can vary in length and number, and may have implications for protein structure, function, or susceptibility to certain diseases.
Amino acid repetitive sequences refer to patterns of amino acids that are repeated in a polypeptide chain. These repetitions can vary in length and can be composed of a single type of amino acid or a combination of different types. In some cases, expansions of these repetitive sequences can lead to the production of abnormal proteins that are associated with certain genetic disorders. The expansion of trinucleotide repeats that code for particular amino acids is one example of this phenomenon. These expansions can result in protein misfolding and aggregation, leading to neurodegenerative diseases such as Huntington's disease and spinocerebellar ataxias.
Microsatellites, also known as short tandem repeats (STRs), are repetitive DNA sequences composed of 1-6 base pair motifs that are repeated in a head-to-tail manner, with repeat lengths varying among individuals, and are widely distributed across the genome, making them useful for forensic identification, gene mapping, and disease diagnosis.
Microsatellite repeats, also known as short tandem repeats (STRs), are repetitive DNA sequences made up of units of 1-6 base pairs that are repeated in a head-to-tail manner. These repeats are spread throughout the human genome and are highly polymorphic, meaning they can have different numbers of repeat units in different individuals.
Microsatellites are useful as genetic markers because of their high degree of variability. They are commonly used in forensic science to identify individuals, in genealogy to trace ancestry, and in medical research to study genetic diseases and disorders. Mutations in microsatellite repeats have been associated with various neurological conditions, including Huntington's disease and fragile X syndrome.
"An amino acid sequence is the specific linear arrangement of amino acids along a polypeptide chain, determined by the genetic code of an organism, that contributes to the unique three-dimensional structure and functional properties of proteins."
An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.
Molecular cloning is a laboratory technique used to produce multiple copies of a specific DNA segment of interest, achieved through the isolation, amplification and subsequent insertion of the target DNA fragment into a self-replicating vector, such as a plasmid or phage, followed by its introduction and propagation in a suitable host organism, like bacteria or yeast.
Molecular cloning is a laboratory technique used to create multiple copies of a specific DNA sequence. This process involves several steps:
1. Isolation: The first step in molecular cloning is to isolate the DNA sequence of interest from the rest of the genomic DNA. This can be done using various methods such as PCR (polymerase chain reaction), restriction enzymes, or hybridization.
2. Vector construction: Once the DNA sequence of interest has been isolated, it must be inserted into a vector, which is a small circular DNA molecule that can replicate independently in a host cell. Common vectors used in molecular cloning include plasmids and phages.
3. Transformation: The constructed vector is then introduced into a host cell, usually a bacterial or yeast cell, through a process called transformation. This can be done using various methods such as electroporation or chemical transformation.
4. Selection: After transformation, the host cells are grown in selective media that allow only those cells containing the vector to grow. This ensures that the DNA sequence of interest has been successfully cloned into the vector.
5. Amplification: Once the host cells have been selected, they can be grown in large quantities to amplify the number of copies of the cloned DNA sequence.
Molecular cloning is a powerful tool in molecular biology and has numerous applications, including the production of recombinant proteins, gene therapy, functional analysis of genes, and genetic engineering.
Trinucleotide Repeat Expansion is a genetic mutation characterized by the abnormal increase in the number of repeated sequences of three DNA nucleotides (trinucleotide repeats), which can lead to various neurological and genetic disorders when exceeding a pathological threshold.
Trinucleotide Repeat Expansion is a genetic mutation where a sequence of three DNA nucleotides is repeated more frequently than what is typically found in the general population. In this type of mutation, the number of repeats can expand or increase from one generation to the next, leading to an increased risk of developing certain genetic disorders.
These disorders are often neurological and include conditions such as Huntington's disease, myotonic dystrophy, fragile X syndrome, and Friedreich's ataxia. The severity of these diseases can be related to the number of repeats present in the affected gene, with a higher number of repeats leading to more severe symptoms or an earlier age of onset.
It is important to note that not all trinucleotide repeat expansions will result in disease, and some people may carry these mutations without ever developing any symptoms. However, if the number of repeats crosses a certain threshold, it can lead to genetic instability and an increased risk of disease development.
'Dinucleotide Repeats' in genetics refer to a pair of consecutive, identical nucleotides that are repeated and adjacent to each other, forming a short repetitive DNA sequence stretch, which, when expanded beyond normal length, can contribute to genetic disorders like fragile X syndrome.
Dinucleotide repeats are a type of simple sequence repeat (SSR) in DNA, which consists of two adjacent nucleotides that are repeated in tandem. In the case of dinucleotide repeats, the repetitive unit is specifically a pair of nucleotides, such as "AT" or "CG." These repeats can vary in length from person to person and can be found throughout the human genome, although they are particularly prevalent in non-coding regions.
Expansions of dinucleotide repeats have been associated with several neurological disorders, including Huntington's disease, myotonic dystrophy, and fragile X syndrome. In these cases, the number of repeat units is unstable and can expand over generations, leading to the onset of disease. The length of the repeat expansion can also correlate with the severity of symptoms.
'Sequence analysis, DNA' refers to the systematic examination and interpretation of the order of nucleotides in a DNA molecule to infer genetic information, such as gene structure, function, evolutionary relationships, and mutations, using various computational methods and tools.
DNA Sequence Analysis is the systematic determination of the order of nucleotides in a DNA molecule. It is a critical component of modern molecular biology, genetics, and genetic engineering. The process involves determining the exact order of the four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - in a DNA molecule or fragment. This information is used in various applications such as identifying gene mutations, studying evolutionary relationships, developing molecular markers for breeding, and diagnosing genetic diseases.
The process of DNA Sequence Analysis typically involves several steps, including DNA extraction, PCR amplification (if necessary), purification, sequencing reaction, and electrophoresis. The resulting data is then analyzed using specialized software to determine the exact sequence of nucleotides.
In recent years, high-throughput DNA sequencing technologies have revolutionized the field of genomics, enabling the rapid and cost-effective sequencing of entire genomes. This has led to an explosion of genomic data and new insights into the genetic basis of many diseases and traits.
Protein tandem repeats
... can be either detected from sequence or annotated from structure. Specialized methods were built for the ... a database of annotated tandem repeat protein structures (CS1 maint: multiple names: authors list, Protein tandem repeats, ... An array of protein tandem repeats is defined as several (at least two) adjacent copies having the same or similar sequence ... In proteins, a "repeat" is any sequence block that returns more than one time in the sequence, either in an identical or a ...
Toroid repeat proteins
"Tandem repeats in proteins: from sequence to structure". Journal of Structural Biology. 179 (3): 279-88. doi:10.1016/j.jsb. ... In the case when the N- and C-terminal repeats lie in close physical contact in a tandem repeat domain, the result is a ... A toroid repeat is a protein fold composed of repeating subunits, arranged in circular fashion to form a closed structure. ... In the case of WD40 repeats (perhaps the largest family of closed solenoids) the number of repeats can range from 4 to 10 (more ...
Major intrinsic proteins
Wistow GJ, Pisano MM, Chepelinsky AB (1991). "Tandem sequence repeats in transmembrane channel proteins". Trends Biochem. Sci. ... The 6 TMS domains are believed to have arisen from a 3-spanner-encoding genetic element by a tandem, intragenic duplication ... Reizer J, Reizer A, Saier Jr MH (1993). "The MIP family of integral membrane channel proteins: sequence comparisons, ... The third subfamily, with little conserved amino acid sequences around the NPA boxes, include 'superaquaporins' (S-aquaporins ...
List of protein tandem repeat annotation software
Jorda, Julien; Kajava, Andrey V. (2009-10-15). "T-REKS: identification of Tandem REpeats in sequences with a K-meanS based ... "Ab initio detection of fuzzy amino acid tandem repeats in protein sequences". BMC Bioinformatics. 13 (3): S8. doi:10.1186/1471- ... A rapid filter for enrichment of sequence datasets with proteins containing tandem repeats". Journal of Structural Biology. 186 ... A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences". BMC Bioinformatics ...
Beta solenoid
RepeatsDB β-solenoid class Kajava AV (September 2012). "Tandem repeats in proteins: from sequence to structure". Journal of ... Beta solenoids are part of the solenoid class of protein tandem repeats. Beta solenoids are elongated and potentially open- ... where the beta sheets are formed by sequences of consecutive repeat units. ... A beta solenoid is a protein fold composed of repeating beta strands subunits, arranged in antiparallel fashion to form a ...
Direct repeat
Tandem repeats (tandem repeat sequences) are repeated copies which lie adjacent to each other. These can also be direct or ... Flanking (or terminal) repeats (terminal repeat sequences) are sequences that are repeated on both ends of a sequence, for ... Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence. In other words, the ... Thus direct repeat tandem sequences are a form of microsattelite DNA. The process of DNA mismatch repair plays a prominent role ...
Caenorhabditis nigoni
Subirana, Juan A.; Messeguer, Xavier (2017-11-28). "Evolution of Tandem Repeat Satellite Sequences in Two Closely Related ... and inter-chromosomal sequence rearrangements. These rearrangements are likely to impede meiotic recombination between ...
Ribosomal DNA
5S tandem repeat sequences in several Drosophila were compared with each other; the result revealed that insertions and ... Cell lines can become malignant from either a rearrangement of the tandem repeats, or an expansion of the repeats in the rDNA. ... In rDNA, the tandem repeats are mostly found in the nucleolus; but heterochromatic rDNA is found outside of the nucleolus. ... As shown in the figure, rDNA of eukaryotes consists of a tandem repeat of a unit segment, composed of NTS, ETS, 18S, ITS1, 5.8S ...
Minisatellite
... and microsatellites are often referred to as short tandem repeats (STRs) or simple sequence repeats (SSRs). Minisatellites ... and that was subsequently identified as large centromeric tandem repeats. When shorter (10-30-bp) tandem repeats were later ... The human telomere sequence itself is a tandem repeat: TTAGGG TTAGGG TTAGGG ... Minisatellites have been implicated[citation ... with the discovery of tandem iterations of simple sequence motifs, the term microsatellites was coined. Microsatellite Tandem ...
Spatial transcriptomics
Thus, these nanoballs comprise numerous tandem repeats of the cDNA sequence. Then sequencing is performed via SOLiD sequencing ... RCAs consist of repeats of the padlock probe sequence. These DNA molecules are then subjected to sequencing by ligation, ... Another way, barcode-targeted sequencing, DNA circularization of a padlock probe with a barcode sequence is conducted by ... Captured RNA is amplified and sequenced. Transcript localization is determined by the barcode oligonucleotide sequence from the ...
Molecular-weight size marker
Microsatellites Also known as SSR (simple sequence repeats) or STR (short tandem repeats), microsatellites differ from ... Minisatellites are short sequences of tandem repeats, approximately 10-60 base pairs. Minisatellites can be used in DNA ... Sequencing is much faster and more efficient. The analysis is automated, as it uses a technique known as shotgun sequencing. ... The second method employs the use of restriction enzymes and a recognized DNA sequence. The DNA is digested by a particular ...
PRP36
A few different tandem repeats, separated repeats, and repeated sequences exist throughout PRP36. These repeats are observable ... Two highly positive sequences exist towards the N terminus of PRP36 while a highly negative sequence exists within the DUF4596 ... PRP36 is highly conserved across primates, but a few short sequences unique to the human version of the gene do exist. Based on ... No signal peptide or other marker is predicted to exist with the PRP36 sequence. However, according to Phobius, PRP36 is ...
Super-enhancer
Gruss P, Dhar R, Khoury G (February 1981). "Simian virus 40 tandem repeated sequences as an element of the early promoter". ... Banerji J, Rusconi S, Schaffner W (December 1981). "Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences ... Benoist C, Chambon P (March 1981). "In vivo sequence requirements of the SV40 early promoter region". Nature. 290 (5804): 304- ... A similar enrichment in disease-associated sequence variation has also been observed for stretch enhancers. Super-enhancers may ...
Ichthyophthirius multifiliis
"Variation in primary sequence and tandem repeat copy number among i-antigens of Ichthyophthirius multifiliis". Molecular and ... Total fish removal and repeated transfer to clean tanks may be applied. Theronts, the motile and fish-infecting stage of the ...
Repeated sequence (DNA)
Tandem repeats are repeated sequences which are directly adjacent to each other in the genome. Tandem repeats may vary in the ... When the repeating sequence is only 2-10 nucleotides long, the repeat is referred to as a short tandem repeat (STR) or ... Tandem repeats and interspersed repeats are further categorized into subclasses based on the length of the repeated sequence ... Interspersed repeats are distinguished from tandem repeats in that the repeated sequences are not directly adjacent to each ...
YWHAQ
UTR a 6 bp tandem repeat sequence that is polymorphic; however, there is no correlation between the repeat number and the ... "Large-scale concatenation cDNA sequencing". Genome Res. 7 (4): 353-8. doi:10.1101/gr.7.4.353. PMC 139146. PMID 9110174. Dubois ...
Penicillium chrysogenum
"The penicillin gene cluster is amplified in tandem repeats linked by conserved hexanucleotide sequences". Proceedings of the ... Observations of morphology and microscopic features are needed to confirm its identity and DNA sequencing is essential to ... Some high-producing Penicillium chrysogenum strains used for the industrial production of penicillin contain multiple tandem ...
Penicillium rubens
"The penicillin gene cluster is amplified in tandem repeats linked by conserved hexanucleotide sequences". Proceedings of the ... Whole genome sequence and phylogenetic analysis, particularly using β-tubulin sequences, in 2011 showed that P. notatum is P. ... "Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum". BMC Genomics. 15 (Suppl 1): S11. ... "Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum". Nature Biotechnology. 26 (10): 1161-1168. ...
Hyalin
Within its sequence is a region containing tandem repeats of about 84 amino acids. This sequence is highly conserved between ... The tandem repeat region was then found to be on the filamentous part of hyalin when the antibodies bound to it. As many as 21 ... These repeats shows no resemblance to anything within the genbank, making hyalin a unique protein. Hyalin is located in the ... A recombinant part of this sequence was created and its adhesive properties were tested. It was found to be about as adhesive ...
Structural motif
Sequence motif Short linear motif Protein tandem repeats Johansson, M.U. (23 July 2012). "Defining and searching for structural ... Cruciform DNA Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a ... Structural motifs may also appear as tandem repeats. Beta hairpin Extremely common. Two antiparallel beta strands connected by ... it can be represented by different and completely unrelated sequences in different proteins or RNA. Depending upon the sequence ...
Human genetic variation
A tandem repeat is the adjacent repetition of a short nucleotide sequence. Tandem repeats exist on many chromosomes, and their ... A variable number tandem repeat (VNTR) is the variation of length of a tandem repeat. ... Short tandem repeats (about 5 base pairs) are called microsatellites, while longer ones are called minisatellites. The recent ... SNPs are the most common type of sequence variation, estimated in 1998 to account for 90% of all sequence variants. Other ...
Borg (microbiology)
Tandem direct repeat sequences are prevalent throughout a Borg's genome, and long inverted repeats terminate the genome. This ... Schoelmerich MC, Sachdeva R, West-Roberts J, Waldburger L, Banfield JF (January 2023). "Tandem repeats in giant archaeal Borg ... Pennisi E (15 July 2021). "Mysterious DNA sequences, known as 'Borgs,'recovered from California mud". Science. Rayne E (2021-08 ... Borgs are long DNA sequences existing alongside the main chromosome in the archaea Methanoperedens, in oxygen-starved ...
Genome
... tandem repeats and interspersed repeats. Short, non-coding sequences that are repeated head-to-tail are called tandem repeats. ... Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome. Tandem repeats can be functional. For ... Usdin K (July 2008). "The biological effects of simple tandem repeats: lessons from the repeat expansion diseases". Genome ... New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing ...
Mucin-16
All mucins contain a tandem repeat domain that has repeating amino acid sequences high in serine, threonine and proline. The C- ... An N-terminal domain A tandem repeat domain A C-terminal domain The N-terminal and tandem repeat domains are both entirely ... an extracellular superstructure dominated by repeat sequences". Tumour Biology. 22 (6): 348-66. doi:10.1159/000050638. PMID ...
Telomeric repeat-containing RNA
Telomerase is the ribonucleoprotein responsible for adding species-dependent tandem repeat sequences (TTAGGG in humans) to the ... Within these CpG island are three repetitive DNA tracts occurring in sequence: a centromere-proximal tract of repeated 61-base- ... This direct inhibitor function acts through base-pairing of the tandem repeats found throughout TERRA's 3'-end to the ... just before the tandem repeats of the telomere begin. In humans, at least 20 of 23 chromosome ends have been shown to contain ...
Diagnostic microbiology
"Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) and Tandem Repeat Sequence Typing (TRST), helpful tools for ... Multilocus sequence typing (MLST) is the sequencing of numerous loci to diagnose an organism by comparing DNA sequences to a ... Multiple-locus VNTR analysis is a test used to detect variable number tandem repeats, which act as a DNA fingerprint in ... Single-locus sequence typing (SLST) is the sequencing of a single locus of an organism to produce data that can be used for ...
Glycoprotein Ib-IX-V complex
These leucine rich repeat sequences tend to be about 24 amino acids in length either occurring singly or in tandem repeats ... Furthermore, there are seven tandem leucine rich repeats and their flanking sequences in the central parallel β-coil region. ... The extracellular domain, which also only has a single leucine rich repeat sequence shares more than 45% sequence identity with ... Following the leucine rich repeat domain is the acidic residue-rich sequence containing sulfated tyrosines, the highly O- ...
Human polyomavirus 2
"Transcription factor Spi-B binds unique sequences present in the tandem repeat promoter/enhancer of JC virus and supports viral ... It is thought that these differences in promoter sequence contribute to the fitness of the virus in the CNS and thus to the ... The protein encoded by these early sequences, T-antigen, also plays a key role in viral proliferation, directing the initiation ... Analysis of the JCVM variant revealed archetype-like regulatory regions with no mutations in coding sequences. The precise ...
STR analysis
The system of DNA profiling used today is based on PCR and uses simple sequences or short tandem repeats (STR). This method ... A short tandem repeat is a microsatellite with repeat units that are 2 to 7 base pairs in length, with the number of repeats ... Short tandem repeat (STR) analysis is a common molecular biology method used to compare allele repeats at specific loci in DNA ... Instead, polymerase chain reaction (PCR) is employed to discover the lengths of the short tandem repeats based on the length of ...
Slipped strand mispairing
Genomic regions with a high proportion of repeated DNA sequences (tandem repeats, microsatellites) are prone to strand slippage ... tandem repeats) are found at the site of replication. Tandem repeats are unstable regions of the genome where frequent ... Simple repetitive DNA sequences containing a variety of adjacent short tandem repeats are commonly observed in non-protein ... Tandem repeats (the main influence for slippage replication) can be found in coding and non-coding regions. If these repeats ...
The MISO Sequence Ontology Browser - TANDEM REPEAT
NanoSTR: A Method for Detection of Target Short Tandem Repeats Based on Nanopore Sequencing Data | Research Square
Short tandem repeats (STRs) are widely present in the human genome. Studies have confirmed that STRs are associated with more ... Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data. Bioinformatics 2019, 35: ... accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION ... Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in ...
Table 2 - Novel Lineage of Methicillin-Resistant Staphylococcus aureus, Hong Kong - Volume 15, Number 12-December 2009 -...
Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats
However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. Tandem repeats, which ... However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. Tandem repeats, which ... Our result suggests that PM exposure is associated with hypomethylation of selected tandem repeats. Measuring tandem-repeat ... Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats Environ Mol Mutagen. 2014 ...
Protein tandem repeats - Wikipedia
Protein tandem repeats can be either detected from sequence or annotated from structure. Specialized methods were built for the ... a database of annotated tandem repeat protein structures (CS1 maint: multiple names: authors list, Protein tandem repeats, ... An array of protein tandem repeats is defined as several (at least two) adjacent copies having the same or similar sequence ... In proteins, a "repeat" is any sequence block that returns more than one time in the sequence, either in an identical or a ...
Cell transformation by FLT3 ITD in acute myeloid leukemia involves oxidative inactivation of the tumor suppressor protein...
Genomic insights into the evolution of Echinochloa species as weed and orphan crop | Nature Communications
... and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative ... Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999). ... Tandem repeat finder (v4.09)74 was used to identify tandem repeats along the chromosomes. To identify the centromeric regions, ... 3). Centromeric regions could be found in all chromosomes containing a 155-bp tandem repeat, similar to other grass species23, ...
NanoSatellite: Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read...
Peter VAN HEUSDEN | University of the Western Cape, Cape Town | uwc | South African National Bioinformatics Institute (SANBI) |...
RepeatMasker output file tabulating the masking results for vertebrate repeat sequences (A)* and for Asian seabass-specific ... These sequencing methodologies provide an opportunity for in-depth analyses of host and pathogen genomes as they are able to ... Tandem repeats with highest coverage of 23-mer HiSeq reads. (XLSX). View ... Whole Genome Sequencing (WGS) is a powerful method for detecting drug resistance, genetic diversity and transmission dynamics ...
ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits | Journal of Molecular Medicine
Numbers below each feature refer to amino acid positions [11, 12, 21]. b Consensus sequence of the tandem repeat. The repeats ... including a large tandem repeat domain (TRD), three short predicted coiled-coil domains and a stretch of ~ 130 residues at the ... a large gene with a tandem repeat encoding 47 amino acids, causes Alström syndrome. Nat Genet 31:79-83 ... Sequence features of ALMS1. a Representation of the primary structure showing recognised features in relation to exon ...
Polymerase Chain Reaction (PCR): Principle and Applications | IntechOpen
... simple sequence repeats) or STRs (short tandem repeats) consist of a few nucleotides-2-6 base pair DNA sequence-epeated several ... VNTRs and STRs are repetitive polymorphisms composed of sequences that are repeated in tandem. These repeat sequences measure ... Among these markers are minisatellites (or variable number of tandem repeats) and microsatellites (or STR, short tandem repeats ... It is therefore necessary to isolate and purify the sequence or sequences that are of interest, whether it is the sequence of a ...
Scientific articles using BIONUMERICS | BIONUMERICS
Typing Clostridium difficile strains based on tandem repeat sequences. BMC Microbiology, 9, 6. DOI link. ... Schouls, LM, van der Heide, HGJ, Vauterin, L, Vauterin, P, & Mooi, FR (2004). Multiple-locus variable-number tandem repeat ... Multilaboratory Validation Study of Standardized Multiple-Locus Variable-Number Tandem Repeat Analysis Protocol for Shiga Toxin ... producing Klebsiella pneumoniae Sequence Type 716: A Study Using Whole-genome Sequencing. Clinical infectious diseases, 68, 993 ...
Volume 2021 Issue 32e20 | Ursus
Tularemia: Practice Essentials, Background, Pathophysiology
Publikationen | Max-Planck-Institut für molekulare Genetik
Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing. bioRxiv (Preprint Server), ... Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data. Bioinformatics 37 (21), S. ... a raw data simulator for Nanopore Sequencing. In: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), ...
Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish...
BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR ... The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for ... The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and ... we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. A total of 176,485 high ...
Impact of Specific Antibiotic Therapies on the prevalence of hUman host ResistaNt bacteria | SATURN | Project | News &...
Multilocus Variable Number of tandem repeat assay and multilocus sequence typing (MLST) analysis was used for molecular ... The Multilocus Variable Number of tandem repeat assays and clustering was performed as previously described. Reference isolates ... Complete nucleotide sequence of KPC-3-encoding plasmid pKpQIL in the epidemic Klebsiella pneumoniae sequence type 258. Leavitt ... We reported the draft genome sequence of the K. pneumoniae ST258 XDR clinical strain from Israel.. Draft Genome Sequence of an ...
Pathophysiological Implication of Vitamin D in Diabetic Kidney Disease | Kidney and Blood Pressure Research | Karger Publishers
Leading-edge Biotechnology Research Group | Cellular and Molecular Biotechnology Research Institute Web Site
Discovery by metagenomics of a functional tandem repeat sequence that controls gene expression in bacteria.. FEMS MICROBIOL ... Draft Genome Sequence of Bryobacteraceae Strain F-183.. MICROBIOL RESOUR ANNOUNC. 2022 Jan 13:e0045321. doi: 10.1128/mra.00453- ... Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1. DNA Res ... Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater.. ...
Frontiers | Comparison of Behavior and Genetic Structure in Populations of Family and Kenneled Beagles
The analyzed STR markers are 90-350 bp long non-transcriptional variable number of tandem repeat sequences at certain points of ... The chromosome localization, repeat structure and PCR primer sequences of the analyzed markers are summarized in Supplementary ... International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. (2001) 409:860- ... The test is repeated once more with the same setup.. Threatening Approach. O stands motionless next to the dog and holds the ...
Molecular Changes in Second Primary Lung and Breast Cancers after Therapy for Hodgkin's Disease1 | Cancer Epidemiology,...
Microsatellites, which are short tandem repeat DNA sequences, are abundantly and evenly distributed throughout the genome. ... The minisatellite repeat sequences examined were as follows: (a) tracts of(A)10 sequence at TGF-βRII; (b)(G)8 at IGFIIR; (c)(G) ... Shibata D., Peinado M. A., Ionov Y., Malkhosyan S., Perucho M. Genomic instability in repeated sequences is an early somatic ... Whereas lengthy microsatellite sequences are uncommon in coding regions, smaller repeats (minisatellites) are occasionally ...
Genomia: Testing of cats: Genetic profile DNA
CareDx Showcases Latest Advances Across AlloSeq Lab Products Portfolio at the 36th European Immunogenetics and...
Comparison of Next-Generation Sequencing and Short-Tandem Repeats to Monitor Chimerism Analysis. ... Detection of HLA-A and HLA-J haplotype diversity from next-generation sequencing data in commercially available samples. ... and clinicians with its best-in-class product portfolio of next-generation sequencing (NGS) based AlloSeq* products, which ...
Recent advances in triple negative breast cancer: the immunotherapy era | BMC Medicine | Full Text
Kyei-Poku, G. | Canadian Forest Service Publications | Natural Resources Canada
Kristín Edda Gylfadóttir, Author at Matís - Page 3 of 7
2018) using expressed sequence tag-short tandem repeats (EST-STRs) markers. Samples (N = 291) were analysed from six sample ... The enzyme shows low sequence identity (,30%) to the members of the type-A family of DNA polymerases, except for two yet ... Using 16S ribosomal RNA gene amplicon sequencing and metagenomics, we resolved the microbial community composition on the North ... then assigned to a species by sequencing 450bp of the Mitochondrial Control Region. Comparing the results with visual ...
Frontiers | Isolation, Molecular Typing, and Antibiotic Susceptibility Testing of Mycobacterium avium Subspecies hominissuis...
All colonies, regardless of the nucleotide sequence of rpsA, were found to be sensitive to all of the drugs tested except for ... All colonies, regardless of the nucleotide sequence of rpsA, were found to be sensitive to all of the drugs tested except for ... MIRU-VNTR analysis, on the other hand, uses mini-satellite sequences (tandem repeats of 10-100 nucleotides) dispersed at ... tandem repeat sequences dispersed at eight loci in the genome as source of genetic variability-in order to find additional ...
Genomics in Medicine Flashcards
Microsatellites (Short sequence repeats, SSRs, Short tandem repeats): are short (1-6bp) repeating sequences in genetic code. ... L1 line sequence transpositions. The idea is that unequal transfer occurs and then a chromosome has two copies of the same gene ... This is an mRNA sequence that codes for more than one protein. ...
Effect of ATRX and G-Quadruplex Formation by the VNTR Sequence on α-Globin Gene Expression - JASCO
ATRX can bind the variable number of tandem repeats (VNTR) sequence in the promoter region of the α-globin gene cluster. The ... Effect of ATRX and G-Quadruplex Formation by the VNTR Sequence on α-Globin Gene Expression. By Yue Li, Junetha Syed, Yuki ... Home / KnowledgeBase Articles / Effect of ATRX and G-Quadruplex Formation by the VNTR Sequence on α-Globin Gene Expression ... Our results demonstrate that stable G-quadruplex formation by the VNTR sequence downregulates the expression of α-globin genes ...
MicrosatellitesLociSSRsNext-Generation SequencingNucleotide sequencesRepetitive sequencesSingle nucleotide pGeneticGenomicGenomesBioinformaticsVNTRSTRsGenesAmino acid sequencesCharacterizationNanoporeChromosomeMethylationSimilarityAnalysisGenome sequenceMicrosatelliteLocusShortVariableFoodborneDataSamplesPutativeDetectionVitroMultigene familiesOutbreakBiologicalSurveillancePatternsSpeciesProteinStrainsAmountsBaseUnitsFamiliesFound
Microsatellites7
- 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)
Loci7
- 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)
SSRs3
- 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)
Next-Generation Sequencing4
- 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)
Nucleotide sequences4
- 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)
Repetitive sequences4
- 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)
Single nucleotide p2
- 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)
Genetic5
- 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)
Genomic9
- 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)
Genomes4
- 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)
Bioinformatics3
- 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)
VNTR3
- 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)
STRs4
- 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)
Genes3
- 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)
Amino acid sequences3
- 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)
Characterization4
- 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)
Nanopore7
- 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)
Chromosome2
- 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)
Methylation2
- 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)
Similarity1
- 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)
Analysis4
- 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)
Genome sequence2
- 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)
Microsatellite1
- 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)
Locus1
- The alleles of STR locus change according to the number of repeats of the given sequence motive. (genomia.cz)
Short5
- 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)
Variable1
- 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)
Foodborne2
- 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)
Data5
- 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)
Samples1
- Besides, NanoSTR also showed 86.36% and 73.48% concordance using the standard samples 9948 and 2800M with MinION sequencing platform, respectively. (researchsquare.com)
Putative1
- 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)
Detection1
- Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. (cdc.gov)
Vitro1
- Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
Multigene families1
- Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
Outbreak1
- Harmonization of whole-genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci. (applied-maths.com)
Biological1
- 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)
Surveillance1
- 4. Expert opinion on whole genome sequencing for public health sur- ratory surveillance. (who.int)
Patterns1
- 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)
Species2
- 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)
Protein2
- 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)
Strains1
- 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)
Amounts1
- 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)
Base2
- 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)
Units3
- 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)
Families1
- However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. (nih.gov)
Found1
- 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)