Deletion repetitive sequences nucleic acid. Medical search. Frequent questions

D-Genies - Specializes in interactive whole genome dotplots of large genomes Dotlet - Provides a program allowing you to construct a dot plot with your own sequences. (wikipedia.org)
LRS can sequence parts of the genome that cannot easily be sequenced by short-read sequencing. (phgfoundation.org)
The genome of most organisms (including humans) is too long to be sequenced as one continuous string. (phgfoundation.org)
Genome assembly: The human genome is over three billion DNA base pairs in length and contains many repetitive stretches of genetic code. (phgfoundation.org)
There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (lookformedical.com)
We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. (biomedcentral.com)
Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. (biomedcentral.com)
We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. (bvsalud.org)
Here, we performed long-read whole-genome sequencing on 10 familial and 9 singleton cases with type I ATD proven by functional and antigen assays, who were selected from a cohort of 340 patients with this rare disorder because genetic analyses were either negative, ambiguous, or not fully characterized. (bvsalud.org)
The resulting sequences can differ from the genome, they exist independently from a particular human genome build, and so must be aligned to the genome to create a track. (ucsc.edu)
3, 137-155 (1996) REFERENCE 9 AUTHORS Fujita,N., Mori,H., Yura,T. and Ishihama,A. TITLE Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region JOURNAL Nucleic Acids Res. (nig.ac.jp)
When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. (noncode.org)
We sequenced and assembled ~49 Mb into 15 super-scaffolds covering 92.83% of the M. phaseolina genome. (biomedcentral.com)
PCR-based testing outweighs all alternatives, as sequencing devices are more expensive, other technologies aimed at examining genome complexity without PCR are expected to gain traction in the coming years. (medicalbuyer.co.in)
DOE JGI in Walnut Creek, California, provides state-of-the-science capabilities for genome sequencing and analysis. (ornl.gov)
The report urges DOE and the Nation to commit to a large, multi-year, multidisciplinary, technological undertaking to order and sequence the human genome. (ornl.gov)
The actual ordering and sequencing involves the coordinated processing of some 3 billion bases from a reference human genome. (ornl.gov)
As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
The Functional Genomics Core facility provides infrastructure for unbiased Target Discovery by means of genome-wide genetic screening in cultured Next Gen Sequencing. (netlify.app)
We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. (stanford.edu)
However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. (frontiersin.org)
We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. (frontiersin.org)
However, in the midst of this process of genome editing, small deletions and insertions might be introduced at the junction site. (springeropen.com)

Five individuals also had interspersed patches of proximal or distal repeat specific DNA sequence indicating potential gene conversion during the exchange of genetic material. (nih.gov)
Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
To overcome these limitations, ongoing advancements in genetic and genomic studies have facilitated the rapid and sensitive identification of infectious diseases, using nucleic acid detection-focused molecular diagnostic tools. (medicalbuyer.co.in)
This effort will first require significant innovation in general capability to manipulate DNA, major new analytical methods for ordering and sequencing, theoretical developments in computer science and mathematical biology, and great expansions in our ability to store and manipulate the information and to interface it with other large and diverse genetic databases. (ornl.gov)
Taxonomic classification of those E. ictaluri specific phages must rely on a synthesis of morphological and genomic details, taking into consideration that phage evolution continues to be profoundly directed by lateral gene transfer, and that a rational hierarchical technique of phage classification really should be based within the degree of DNA and protein sequence identity for several genetic loci. (hivprotease-signal.com)

Insertions and deletions between sequences give rise to disruptions in this diagonal. (wikipedia.org)
Frame shifts include insertions, deletions, and mutations. (wikipedia.org)
Variant detection: Some features of individual genomes are particularly difficult to detect and quantify with SRS technologies, for example: large and complex rearrangements, large insertions or deletions of DNA, repetitive regions, highly polymorphic regions, or regions with low DNA nucleotide diversity. (phgfoundation.org)
This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) - collectively Simple Nucleotide Polymorphisms - from dbSNP build 141, available from ftp.ncbi.nih.gov/snp . (noncode.org)

This relationship is affected by certain sequence features such as frame shifts, direct repeats, and inverted repeats. (wikipedia.org)

True LRS technologies - sometimes referred to as third generation sequencers - directly sequence single molecules of DNA in real time, often without the need for amplification. (phgfoundation.org)
This approach resolved, independently of its size or type, all eight SVs detected by multiple ligation-dependent probe amplification, and identified for the first time a complex rearrangement previously misclassified as a deletion. (bvsalud.org)
Remarkably, we identified the mechanism explaining ATD in 2 out of 11 cases with previous unknown defect: the insertion of a novel 2.4 kb SINE-VNTR-Alu retroelement, which was characterized by de novo assembly and verified by specific polymerase chain reaction amplification and sequencing in the probands and affected relatives. (bvsalud.org)
Indeed, if the sequence of interest is present in the DNA extract, it is possible to selectively replicate it (we speak of amplification) in very large numbers. (intechopen.com)
Techniques, such as high-throughput sequencing, polymerase chain reaction, gene chip technology, and isothermal amplification reaction, are widely employed as primary diagnostic methods. (medicalbuyer.co.in)
1994) IRE-bubble PCR: a rapid method for efficient and representative amplification of human genomic DNA sequences from complex sources. (u-tokyo.ac.jp)

OTEs are undesired changes to genomic DNA sequences with some sequence similarity to the target site. (idtdna.com)

Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. (lookformedical.com)
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (lookformedical.com)
Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
Phylogenetic analysis primarily based to the significant terminase subunit amino acid sequence plus the DNA polymerase I amino acid sequence of eiAU reveal that phages eiAU, eiDWS, and eiMSLS were most much like phage that infect other enterobacteria and Sodalis glossinidius. (hivprotease-signal.com)
Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. (biomedcentral.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)
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)

TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (lookformedical.com)

The NGS core offers sequencing on Illumina NextSeq500 and the Oxford nanopore Minion platforms. (netlify.app)
To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. (frontiersin.org)
With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. (frontiersin.org)

The nucleotide and deduced amino acid sequences of the phnA gene showed no significant homology with any data bank accessions. (embl-heidelberg.de)
Sequence homology searches identify PhnC, PhnK, PhnL, and, possibly, PhnN proteins as members of nucleotide-binding proteins of the binding protein-dependent transport systems. (embl-heidelberg.de)
DNA double strand break repair (DSBR) pathways are generally classified based on whether sequence homology is used to join the broken DNA ends. (springeropen.com)
Non-homologous end joining (NHEJ), which does not depend upon sequence homology, is the key repair pathway during the G0/G1 stages of the cell cycle [ 10 ]. (springeropen.com)

With more than 1100 worldwide collaborators on active projects, JGI is the preeminent facility for sequencing plants, microbes, and microbial communities that are foundational to energy and environmental research. (ornl.gov)

Sequences of DNA in the genes that are located between the EXONS. (lookformedical.com)
The NCBI RefSeq Genes composite track shows zebrafish protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). (ucsc.edu)
Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B. (embl-heidelberg.de)

the invention also provides non-human animals and cells comprising a transgene encoding an APP comprising the Swedish mutation and further comprising functionally disrupted endogenous APP gene loci, transgenes and targeting constructs used to produce such transgenic cells and animals, transgenes encoding human Swedish mutation APP polypeptide sequences, and methods for using the transgenic animals in pharmaceutical screening and as commercial research animals for modeling neurodegenerative diseases (e.g. (justia.com)
Complementation analysis using deletion derivatives of the 3.5-kilobase fragment showed that the gene mutated in EF116, which we designate hetA, lies within this ORF. (agri.gov.il)
Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. (ucsc.edu)
The complete nucleotide sequence of 15,611 bases has been determined, and the gene structures were examined. (embl-heidelberg.de)
A Pho box-like promoter sequence is also found upstream of the gene cluster starting at phnA, which is consistent with the observation of phosphate regulation of the Phn+ response. (embl-heidelberg.de)
An unusual finding is that one of the repetitive extragenic palindromic sequences actually overlaps with the reading frame of the phnE gene. (embl-heidelberg.de)
The predicted gene products with sequence similarity amongst the eiAU and SSL 2009a phage genomes include things like the putative small tail proteins tail tape mea certain, major tail proteins, major capsid proteins, head morphogenesis, phage terminase tiny subunit, and the phage terminase large subunit. (hivprotease-signal.com)
The substantial terminase subunit which is a structural protein is together with the portal protein viewed as essentially the most universally conserved gene sequence in phages, consequently they are good possibilities to assist in phage classification. (hivprotease-signal.com)
For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)
The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. (embl.de)
SINE sequences are approximately 70-700 base pairs (bp) averaging about 250 bp [ 1 ] with most organized into an RNA gene-derived region, a di-nucleotide repeat region and terminating in a poly A or poly A/T tail [ 2 - 4 ]. (biomedcentral.com)
One hundred sixteen patients with classical and atypical RTT were studied for mutations of the MeCP2 gene by using DHPLC and direct sequencing. (neurology.org)
The authors found 17 novel mutations, including a complex gene rearrangement found in one individual involving two deletions and a duplication. (neurology.org)

Current technologies for analyzing genomic aberrations in clinical applications include real-time PCR (qPCR), fluorescence in situ hybridization (FISH), microarrays, and next-generation sequencing (NGS). (medicalbuyer.co.in)

The genomic sequences of ten geographically and phenotypically diverse clinical isolates of M. catarrhalis were determined and analyzed together with two publicly available genomes. (biomedcentral.com)
Interestingly, other struc tural proteins which includes the host specificity proteins, the tail assembly proteins, and specifically the tail fiber baseplate protein which has become suggested for exclusion in any sequence based mostly phage taxonomy scheme are certainly not shared in between the 2 genomes. (hivprotease-signal.com)
Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. (biomedcentral.com)

To unravel the mechanisms of repeat instability in nondividing cells, we created an experimental system to analyze the mutability of Friedreich's ataxia (GAA)n repeats during chronological aging of quiescent Saccharomyces cerevisiae Unexpectedly, we found that the predominant repeat-mediated mutation in nondividing cells is large-scale deletions encompassing parts, or the entirety, of the repeat and adjacent regions. (stanford.edu)

Progress has been accelerated by the advancement of high-throughput nextgeneration sequencing (NGS) technologies, which are capable of reading the code of millions of small fragments of DNA in parallel. (phgfoundation.org)
The Functional Genomics Core (FGC) provides capacity for high-throughput chemical, RNAi, and deletion library-based screens for the purpose of network analysis, drug and target discovery. (netlify.app)

Low-copy-number repeat sequences flank the DiGeorge/velo-cardio-facial syndrome loci at 22q11. (ox.ac.uk)

Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (ind.in)
Queen's University QUB Functional Genomics CTU Sanger sequencing Full with Initial PCR (£12/sample). (netlify.app)

An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next. (uams.edu)

In bioinformatics a dot plot is a graphical method for comparing two biological sequences and identifying regions of close similarity after sequence alignment. (wikipedia.org)
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. (wikipedia.org)
For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix. (wikipedia.org)
Some idea of the similarity of the two sequences can be gleaned from the number and length of matching segments shown in the matrix. (wikipedia.org)
Regions of local similarity or repetitive sequences give rise to further diagonal matches in addition to the central diagonal. (wikipedia.org)
The closeness of the sequences in similarity will determine how close the diagonal line is to what a graph showing a curve demonstrating a direct relationship is. (wikipedia.org)
OTEs occur when the Cas enzyme is directed to the wrong site by the gRNA due to such sequence similarity. (idtdna.com)

TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (lookformedical.com)

The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (lookformedical.com)

Core member of Genomics & Genetics Leadership Team charged with defining a The mission of the NHP Functional Genomics Core is to ensure standardization and comparability of functional genomics services and assays conducted for the network analysis, disease association analysis, functional genomics analysis, The sequencing data was generated by the UTHealth Cancer Genomics Core Read the latest Research articles in Functional genomics from Nature. (netlify.app)

DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (lookformedical.com)

and, replacement of G-11499 by T in exon VIII, resulting in an amino acid substitution of Cys430 by Phe. (embl.de)

Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)

Other, 'synthetic' long-read sequencing approaches utilise modified sample processing and conventional SRS to computationally reconstruct long reads from shorter sequencing reads. (phgfoundation.org)
These approaches depend on sequence databases that are used by the engines to match real spectra to theoretical in silico spectra. (lu.se)

Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)

Repetitive short interspersed elements (SINEs) are ubiquitous eukaryotic retrotransposons. (biomedcentral.com)

Both have developed platforms for 'real-time' sequencing of nucleic acids (DNA and RNA) that is faster than current short-read technologies. (phgfoundation.org)

first is the use of 5-25 base pair (bp) microhomologous sequences during the alignment of the broken ends before religating them, and second is the slower kinetics of repair [ 15 ]. (springeropen.com)

They were manually curated, based on publications describing transcripts and manual reviews of evidence which includes EST and full-length cDNA alignments, protein sequences, splice sites and any other evidence available in databases or the scientific literature. (ucsc.edu)

Two pairs of co-dominant polymorphisms were detected, and were converted into sequence-specific PCR markers desirable for routine marker implementation. (cropscience.org.au)

1992) Science 255:728-730, prepared a series of deletion mutants of amyloid precursor protein and observed a single cleavage site within the .beta. (justia.com)

These were introduced by Gibbs and McIntyre in 1970 and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. (wikipedia.org)
We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. (elifesciences.org)
The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. (embl.de)
The amino acid sequences of one of many conserved structural pro teins likewise as among the non structural proteins have been selected for phylogenetic evaluation. (hivprotease-signal.com)

describes the potential of these technologies for diagnostic sequencing in a clinical setting, and in this context the challenges with implementing the technology. (phgfoundation.org)

Deletion analysis demonstrated that at least 13 kilobases of DNA information is required for E. coli to express the phosphonate utilization phenotype (Phn+). (embl-heidelberg.de)
With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)

A 1.7-kb hotspot for homologous recombination was previously identified wherein the relative risk of an exchange event is 50 times higher than in the surrounding 98.7% identical sequence shared by the CMT1A-REPs. To refine the region of exchange further, we designed a PCR strategy to amplify the recombinant CMT1A-REP from HNPP patients as well as the proximal and distal CMT1A-REPs from control individuals. (nih.gov)

Sequences of DNA or RNA that occur in multiple copies. (lookformedical.com)
This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template). (intechopen.com)
A core region of beta-catenin, composed of 12 copies of a 42 amino acid sequence motif known as an armadillo repeat, mediates these interactions. (embl.de)

When the residues of both sequences match at the same location on the plot, a dot is drawn at the corresponding position. (wikipedia.org)
The complement control protein (CCP) modules (also known as short consensus repeats) are defined by a consensus sequence within a stretch of about 60 amino acid residues. (embl.de)

The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. (lu.se)

The two DUX4‐fl isoforms produce the same protein sequence and differ only in the splicing of the 3′UTR. (comprehensivephysiology.com)

Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions. (idtdna.com)
Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)
You can view Archer assays alongside IDT's xGen™ NGS portfolio to find the best next generation sequencing solution for your lab. (idtdna.com)

The HNPP (hereditary neuropathy with liability to pressure palsies) deletion and CMT1A (Charcot-Marie-Tooth disease type 1A) duplication are the reciprocal products of homologous recombination events between misaligned flanking CMT1A-REP repeats on chromosome 17p11. (nih.gov)
Nearly 50 hereditary diseases result from the inheritance of abnormally long repetitive DNA microsatellites. (stanford.edu)

The results suggest a relatively recent evolutionary origin for these sequences and the loss of one sequence during the course of primate evolution. (ox.ac.uk)

The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)

Anatomy22

Organisms23

Diseases5

Chemicals and Drugs68

Analytical, Diagnostic and Therapeutic Techniques and Equipment38

Phenomena and Processes127

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture3

Information Science7

Health Care3

Genome23

Genetic5

Insertions4

Inverted repeats1

Amplification6

Genomic DNA sequences1

Polymerase5

Nucleotide sequences3

TANDEM REPEAT SE1

Nanopore3

Homology4

Microbial1

Genes3

Gene13

Fluorescence1

Genomes3

Mutation1

High-throughput2

Loci1

Sanger2

Tandemly repeated1

Similarity7

Flank1

Humans1

Genomics1

Insertion1

Amino Acid Substitution1

Molecular1

Approaches2

Antibody1

Eukaryotic1

Platforms1

Alignment1

Splice1

Polymorphisms1

Cleavage1

Proteins4

Diagnostic1

Analysis2

Identical1

Copies3

Residues2

Detect1

Differ1

Next generation3

Hereditary2

Results1

Regulatory1