Databases uses high throughput nucleotide sequencing. Medical search. Frequent questions

The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length. (wikipedia.org)
The archive is part of the International Nucleotide Sequence Database Collaboration (INSDC), and run as a collaboration between the NCBI, the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ). (wikipedia.org)
This database is produced at National Center for Biotechnology Information (NCBI) as part of an international collaboration with the European Molecular Biology Laboratory (EMBL) Data Library from the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). (iospress.nl)
This enables researchers and laboratory technicians with limited bioinformatics expertise to scan and analyze raw sequencing data in a matter of minutes. (biomedcentral.com)
Extracting single nucleotide polymorphisms (SNPs), the most widely studied form of genetic variation, from WGS data requires substantial bioinformatics expertise, as well as dedicated bioinformatic analysis pipelines often based on customized scripts. (biomedcentral.com)
RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. (frontiersin.org)
Bioinformatics approaches outlined a low nucleotide identity of P. parmentieri and P. wasabiae with other species, while P. carotovorum subsp. (mdpi.com)
Established in September 2005, this international community includes representatives from the International Nucleotide Sequence Database Collaboration (INSDC), major genome sequencing centers, bioinformatics centers and a range of research institutions. (biomedcentral.com)
Since 2014, the Advanced Molecular Detection (AMD) program has worked to integrate the latest next-generation sequencing technology with bioinformatics and epidemiology expertise to improve public health. (cdc.gov)
As part of the Bioinformatics Core Facility (BCF) at the University of Manchester (UoM) we have developed a number of bespoke Galaxy tools to support local researchers conducting next generation sequencing (NGS) analyses. (tsl.ac.uk)
The main purpose of a bioinformatics platform within SWEGENE should be to provide com- putational facilities and logistical support [databases & infrastructure] for scientists whose primary research in biology and medicine benefit from computational approaches. (lu.se)
Various software resources are also required to enable users to conveniently connect their experimental results with publicly, and application specific, bioinformatics databases and tools. (lu.se)
The purpose of a bioinformatics platform within SWEGENE is to provide computational facilities and logistical support [databases, algorithms & infrastructure] for problem oriented scientists in an optimal way. (lu.se)
Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (cdc.gov)
Sarah Gregory] I understand that the ability of this sequencing to work optimally is dependent on bioinformatics. (cdc.gov)
So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (cdc.gov)
I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (cdc.gov)

Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
To make a reference panel of genomic variation for the Japanese population, we sequenced whole genomes of 1,070 cohort participants, and detected genomic variants including SNVs, indels and structural variants. (nature.com)
Thanks to the latest technological advances, bacterial genomes can now be sequenced in less than 48 hours for less than €100 per genome. (biomedcentral.com)
the first three issues have included "Short Genome Reports" on 32 sequenced bacterial genomes. (biomedcentral.com)
Its focus was on comparative studies of (meta)genomes that bring these sequences into "context" (i.e., by geolocation, habitat, organism phenotype, etc). (biomedcentral.com)
Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. (bvsalud.org)
Lower quality sequences (draft genomes and short metagenomics reads) will be included in future releases. (biomedcentral.com)
We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013-2014 by ARSP. (who.int)

The GenBank direct submissions group also processes complete microbial genome sequences. (iospress.nl)
We developed KvarQ, a new tool that directly scans fastq files of bacterial genome sequences for known variants, such as single nucleotide polymorphisms (SNP), bypassing the need of mapping all sequencing reads to a reference genome and de novo assembly. (biomedcentral.com)
In this article, we demonstrate how KvarQ can be used to successfully detect all main drug resistance mutations and phylogenetic markers in 880 bacterial whole genome sequences. (biomedcentral.com)
Using the allele frequency spectrum of SNVs from 71,702 whole genome sequences in gnomAD, we find that SNVs introducing new stop codons, or creating stronger translation termination signals in uORFs are under strong selective constraints within 5′UTRs. (nature.com)
First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences. (cdc.gov)

Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences. (ox.ac.uk)
The repertoire in humans can now be comprehensively measured by high-throughput sequencing. (ox.ac.uk)
Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. (ox.ac.uk)
The application of TIgGER continues to identify a surprisingly high frequency of novel alleles in humans, highlighting the critical need for this approach. (debian.net)

This approach identified genetic markers (SNPs, or single nucleotide polymorphism) useful for assessing whether germplasm is identical at various positions in the genome. (usda.gov)

Residual amounts of amplified genomic DNA are minimized and do not interfere with mitochondrial-specific downstream methods such as qPCR or direct Sanger sequencing. (qiagen.com)
These technologies have been available since 2004, and they have largely replaced the previous method ("Sanger sequencing") and make high-throughput WGS possible. (cdc.gov)
The results of the multi‑gene panel test were further verified by Sanger sequencing. (spandidos-publications.com)

Currently, general-purpose DNA databases, as provided by the International Nucleotide Sequence Database Collaboration (INSDC [ 3 ]), store only limited environmental contextual (meta-)information with the sequences, if any. (biomedcentral.com)

Identifying individual SNPs of interest usually requires mapping all sequencing reads in a fastq file to a given reference genome, despite the fact that only a few nucleotide positions might be relevant. (biomedcentral.com)

The cost reduction and high-throughput automation of DNA sequencing over the last years have had a profound impact on the field of microbial ecology, giving birth to the field of ecological genomics. (biomedcentral.com)
The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. (routledge.com)

To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea . (springer.com)
In addition, using sequences of three mitochondrial genes, the phylogenetic relationships between every sample with a known karyotype were determined, which revealed significant nucleotide divergence among the karyomorphs. (scielo.br)
Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken. (bvsalud.org)
Phylogenetic analysis showed that the Indian sequences belonged to different clusters. (bvsalud.org)

Clinical whole-exome sequencing for the diagnosis of rare disorders with congenital anomalies and/or intellectual disability: substantial interest of prospective annual reanalysis. (canceropole-est.org)
Solo clinical whole-exome sequencing (WES) was applied in our genetics center to improve diagnosis in patients with CA/ID.MethodsThis retrospective study examined 416 consecutive tests performed over 3 years to demonstrate the effectiveness of periodically reanalyzing WES data. (canceropole-est.org)
To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. (biomedcentral.com)
Whole exome sequencing (WES), involves sequencing of coding exons comprising approximately 2% of the whole human genome, which are estimated to contain approximately 85% of pathogenic variants associated with monogenic disease [ 6 ]. (biomedcentral.com)
Using these variants, we map and validate gene-disease associations in two independent biobanks containing exome sequencing from 10,900 and 32,268 individuals, respectively, and elucidate their impact on protein expression in human cells. (nature.com)
Background De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. (bmj.com)
Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. (bmj.com)

These databases provide resources to analyze the effect of mutations on human health. (hindawi.com)
Either at genomic or at proteomic level, mutations have significant impact on normal gene or protein function, and human diseases could be associated with mutations like nonsynonymous single-nucleotide variations (nsSNVs) on amino acids. (hindawi.com)
Evolving sequence mutations in the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). (cdc.gov)
Next-Generation Sequencing (NGS) remains the tool of choice for whole-genome analysis and deciphering new mutations [3]. (fortunejournals.com)
Mutations with higher transmissibility, a more intense disease state, and less likely to respond to vaccines or treatments have been classified by the World Health Organization (WHO) as Variants of Concern. (fortunejournals.com)
With the development of next-generation sequencing (NGS), research has focused on comprehensive genomic analysis based on tumor molecular features, such as somatic mutations and copy number variation. (spandidos-publications.com)

The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. (iospress.nl)
The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. (edu.au)
In particular, upstream open reading frames (uORFs) are segments of 5′UTR mRNA sequences that can initiate and terminate translation upstream of protein-coding start codons. (nature.com)
Specific uORFs are known to control protein expression by tuning translation rates of downstream protein-coding sequences, and potential uORFs have been identified in ~50% of all human protein-coding genes 1 , 2 . (nature.com)
Ideally, the solution of these protein structures will also contribute to the understanding of protein sequence-structure relationships in general. (nih.gov)
The main problem when using information derived from different databases is to correctly assign different gene, transcript or protein identifiers. (tsl.ac.uk)
We show that human and chimpanzee cells differentiate in a similar man¬ner and that the difference in interspecies protein abundance is higher than transcript-level differences, suggesting that post-transcriptional mechanisms play a role in the difference between human and chim¬panzee brain development. (lu.se)
After 4 weeks of conversion, we performed global analyses of RNA and protein levels by RNA-sequencing and mass spectrometry. (lu.se)

Internally the SRA relies on the NCBI SRA Toolkit, used at all three INSDC member databases, to provide flexible data compression, API access and conversion to other formats such as FASTQ. (wikipedia.org)
European Nucleotide Archive, page for searches in SRA SRA homepage at NCBI. (wikipedia.org)
Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. (irta.cat)
However, because NCBI annotation is for most species the most comprehensive, we need to map information from other databases to EntrezGene IDs. (tsl.ac.uk)

Here we use translated uORFs mapped through ribosome-profiling experiments and a deep catalog of human genetic variation to characterize patterns of selection acting on single nucleotide variants (SNVs) in uORF sequences. (nature.com)
We assess evidence for the functional importance of translation at uORFs, and explore possible phenotypic consequences associated with genetic variation in these sequences. (nature.com)

With the development of high throughput technologies such as tandem mass spectrometry (MS/MS) and next generation sequencing, more and more nonsynonymous single-nucleotide variations (nsSNVs) that cause variation of amino acids have been identified, some of which result in the damage of PTMs. (hindawi.com)
High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. (edu.au)
Next-generation sequencing (NGS) generates large amounts of genomic data and reveals about 20 000 genetic coding variants per individual studied. (nih.gov)
RNA sequencing (RNA-Seq) is a modern technology for transcriptome profiling that uses next-generation sequencing (NGS). (frontiersin.org)
Next-generation sequencing technologies have become important tools for genome-wide studies. (biomedcentral.com)
ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. (biomedcentral.com)
Methods: Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. (bvsalud.org)
Next-generation sequencing (NGS) refers to sequencing technologies that can process a large quantity of genetic material at a time. (cdc.gov)
Some next-generation sequencing devices read fluorescent signals. (cdc.gov)
With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. (rsc.org)
Sarah Gregory] And following on that, what is Next Generation Sequencing? (cdc.gov)
Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (cdc.gov)
Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (cdc.gov)

Some databases such as dbSNP [ 5 ] and SNVDis [ 6 ] curated such mutation data. (hindawi.com)
The volume of data deposited in the Sequence Read Archive has grown rapidly. (wikipedia.org)
Nature Publishing Group journals require that DNA and RNA sequencing data is made available through the SRA. (wikipedia.org)
Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. (iospress.nl)
Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation. (ox.ac.uk)
This service has removed one of the primary bottlenecks in metagenome sequence analysis - the availability of high-performance computing for annotating the data. (edu.au)
http://ijgvd.megabank.tohoku.ac.jp/ ) provides genomic variation data detected by whole-genome sequencing (WGS) of Japanese individuals. (nature.com)
High-throughput DNA sequencing produces vast amounts of data, with millions of short reads that usually have to be mapped to a reference genome or newly assembled. (biomedcentral.com)
Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. (biomedcentral.com)
Here we present a novel R package, ReQON (Recalibrating Quality Of Nucleotides), that recalibrates the quality scores from a BAM file of aligned sequencing data. (biomedcentral.com)
Summary: Infers the V genotype of an individual from immunoglobulin (Ig) repertoire-sequencing (Rep-Seq) data, including detection of any novel alleles. (debian.net)
A key step in analyzing these data involves assignment of the germline V, D and J gene segment alleles that comprise each immunoglobulin sequence by matching them against a database of known V(D)J alleles. (debian.net)
Newer sequencing platforms have revolutionized this field, by generating larger volumes of data and dramatically lowering the cost of sequencing. (cdc.gov)
The sequencer produces data-millions of long strings of letters-which are then assembled together or aligned with a reference sequence. (cdc.gov)
Analytical programs compare the new sequence data to the reference sequence and identify variations in the sample that allow scientists to infer an ancestral relationship, much like a family tree. (cdc.gov)
MetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. (biomedcentral.com)
This clearly hinders integrated ecological interpretations and limits the extraction of biological knowledge from raw sequence data. (biomedcentral.com)
Furthermore, genomic and metagenomic sequence data can be supplemented by information extraction from the literature for proper georeferencing. (biomedcentral.com)
Here we introduce MetaLook, a 3D visualisation software allowing browsing and interpretation of marine sequence data in their ecological context. (biomedcentral.com)
The concept described revolves around the creation of a nation-wide distributed cluster of pathogen-specific databases of NGS and epidemiological data hosted on servers present at each of the participating institutes. (tsl.ac.uk)
The redundancy originated by the replication process is meant to guarantee a distributed access to the Information System, a high availability of the data hosted, a geographically distributed disaster recovery capability and to enable load-balancing of queries at each node, increasing the performance of access to the analytical pipelines in case of heavy traffic on any of the servers. (tsl.ac.uk)
High-quality protocols are then provisionally accepted for publication before data collection commences. (eneuro.org)
Notice for patent related sequence data 4. (nig.ac.jp)
This unified database was made possible thanks to the international collaboration among the three data banks. (nig.ac.jp)
2. DDBJ flat file format The database is a collection of "entry" which is the unit of the data. (nig.ac.jp)
Sarah Gregory] Ok, so what does sequence data in a public health lab do for us? (cdc.gov)
Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)
It allows us to quickly generate huge amounts of data and DNA sequence in a very short period of time. (cdc.gov)
The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. (who.int)

Specifically, the database contains variants detected by WGS of 1,070 individuals who participated in a genome cohort study of the Tohoku Medical Megabank Project. (nature.com)
Therefore, high-coverage WGS of a larger number of individuals for a target population is desired to construct a variant catalogue with reliable allele frequencies, including rare variants. (nature.com)
Moreover, it has been shown that variants destroying stop codons in translated uORFs are under strong negative selection, presumably because the resultant translational readthrough can decrease start codon recognition and translation initiation at the coding sequence (CDS) 10 . (nature.com)
However, the rapid emergence of several variants with higher virulence and infectivity has provoked repeat waves of the deadly pandemic in many countries and raised anxieties about vaccine efficacy and diagnostic accuracy [2]. (fortunejournals.com)

DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. (irta.cat)
He has published numerous original ideas and reports, established standards and guidelines for variations and variation databases and developed tools and performed analyses for the interpretation of variations in several diseases. (lu.se)

We also confirmed that the targeted genes were negatively correlated with the clinical variables related to T2DM in the BxD mouse genetic reference population database. (biomedcentral.com)

For comprehensive investigation of the genetic heterogeneity of diseases with a wide range of causative genes, such as hearing loss, and to identify novel candidate genes, WES analysis overcomes the limitations of targeted analysis and is considerably more cost-effective than whole genome sequencing (WGS) analysis. (biomedcentral.com)
miRNAs, which are short (~ 22 nucleotides) noncoding RNAs, have emerged as key cell type-specific regulators of gene expression, operating primarily to inhibit target genes post-transcription by binding with complementary mRNA [ 12 ]. (biomedcentral.com)
To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. (biomedcentral.com)
So far there is a number of well-organized databases that contain useful information regarding orthologous genes, e.g. (tsl.ac.uk)

Originally called the Short Read Archive, the name was changed in anticipation of future sequencing technologies being able to produce longer sequence reads. (wikipedia.org)
As of September 2010, 65% of the SRA was human genomic sequence, with another 16% relating to human metagenome sequence reads. (wikipedia.org)
13 The sequence reads were mapped onto the human reference genome, assembly GRCh37/hg19, with decoy sequences (hs37d5) and an average sequencing coverage of 32.4× for full-length autosomal chromosomes. (nature.com)

The genome, or genetic material, of an organism is made up of a unique DNA or RNA sequence. (cdc.gov)

With the development of high-throughput sequencing technology, gene mutation detection has become another important resource to investigate regulatory mechanisms and cellular processes. (hindawi.com)

GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. (iospress.nl)

For analysis by HTS, 6 DNA samples extracted from cutaneous swabs obtained from the skin surface of facial areas (forehead and eyebrows) of patients previously studied by PCR for MCPyV sequences were selected ( 5 ). (cdc.gov)
The REPLI-g Mitochondrial DNA Kit overcomes this limitation by enriching for mitochondrial DNA sequences in total DNA samples. (qiagen.com)
In this project, the genomic DNA of 1,070 subjects obtained from peripheral blood samples was subjected to paired-end sequencing using the Illumina HiSeq 2500 platform. (nature.com)
Geographic locations were stored in our database for accepted DNA samples. (biomedcentral.com)

Deep sequencing of Internal Transcribed Spacer (ITS) regions is the de facto standard for fungal diversity analysis. (elsevierpure.com)
We evaluated the efficacy of strategies for mycobiome analysis by using this database and characterizing a mock fungal community consisting of 26 species representing 15 genera using ITS1 sequencing with three HTS platforms: Illumina MiSeq (MiSeq), Ion Torrent Personal Genome Machine (IonPGM), and Pacific Biosciences (PacBio). (elsevierpure.com)
Using this strategy for deep-sequencing analysis of the gut mycobiota in healthy Japanese individuals revealed two major mycobiota types: a single-species type composed of Candida albicans or Saccharomyces cerevisiae and a multi-species type. (elsevierpure.com)
Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2. (bvsalud.org)
The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis. (biomedcentral.com)
The work presented in this thesis focuses on the bioinformatic methods for a TE-centric analysis of next- and third-generation sequencing technologies. (lu.se)

A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity. (cdc.gov)
This FOA encourages applications to establish partnerships between researchers interested in a biological problem of significant scope and researchers providing high-throughput structure determination capabilities through the NIGMS PSI:Biology network. (nih.gov)
However, biological nitrification and denitrification is not the most effective process in nitrogen removal owing to the high oxygen demand of complete nitrification, the heterotrophic denitrification requires an external carbon source, accompanied by the production of sludge and nitrous oxide (N 2 O) (Shalini et al. (springeropen.com)

GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 115,000 distinct organisms. (iospress.nl)
Upon receipt of a sequence submission, the GenBank staff assigns an Accession number to the sequence and performs quality assurance checks. (iospress.nl)
REFERENCE 1 (bases 1 to 450) AUTHORS Mishima,H. and Shizuoka,T. TITLE Direct Submission JOURNAL Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases. (nig.ac.jp)

We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. (biomedcentral.com)
A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome‑wide transcriptional sequencing was performed. (spandidos-publications.com)

We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. (biomedcentral.com)

This database can be utilized for the taxonomic assignment of fungal community members. (elsevierpure.com)
In this study, we proposed the best possible processing strategies for the three sequencing platforms, of which, the PacBio platform allowed for the most accurate estimation of the fungal community. (elsevierpure.com)
GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. (cdc.gov)

Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea . (springer.com)

681,257 SNP markers were distributed across the entire maize genome, and most alleles were detected as rare with high confidence levels. (usda.gov)
This method produced 681,257 SNP markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. (usda.gov)
However, this process will fail for sequences that utilize previously undetected alleles, whose frequency in the population is unclear. (debian.net)
TIgGER is a computational method that significantly improves V(D)J allele assignments by first determining the complete set of gene segments carried by an individual (including novel alleles) from V(D)J-rearrange sequences. (debian.net)

However, results are often biased because of the wide variety of sequence lengths in the ITS regions and the complexity of high-throughput sequencing (HTS) technologies. (elsevierpure.com)
JAX APML integrates the latest sequencing technologies with the insights of an experienced multidisciplinary team of scientists to help clinicians and translational researchers select the best options for personalized care. (jax.org)
The CLIA-certified, CAP-accredited, and NCI-MATCH-designated laboratory features the latest sequencing and PCR technologies. (jax.org)

ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. (lu.se)

Case 4 was a phenotypically isolated case recruited into an undiagnosed rare disorders sequencing study. (bmj.com)

Nevertheless, the functional potential coded in the DNA sequences can be successfully interpreted only if considered in their ecological context. (biomedcentral.com)

This is an important issue for the generation of a Mammalian Ortholog and Annotation Database (MOA-Db) which will be partially based on information from publicly available databases, which needs to be collected, analyzed, and connected. (tsl.ac.uk)

These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. (ox.ac.uk)

Each of these platforms have technological limitations due to sample preparation steps, amount of material needed for sequencing, and sequencing depth requirements. (rsc.org)
Most of the platforms are expected to be connected to resources for handling various types of user interactions, conceivably with a back-end database management system and a front-end web based technique to handle user interactions. (lu.se)

While studying the virome of the skin surface of a patient with a Merkel cell carcinoma (MCC) by using unbiased, high-throughput sequencing, we identified a human polyomavirus nearly identical to human polyomavirus 9, a virus recently reported in blood and urine of renal transplantion patients and closely related to the African green monkey lymphotropic polyomavirus. (cdc.gov)
In this study of the skin virome of a patient with MCC, using high-throughput sequencing (HTS) and comparing sequences from a patient with MCC with sequences from healthy controls, we identified a human polyomavirus strain nearly identical to HPyV9, a virus species closely related to the lymphotropic polyomavirus (LPV). (cdc.gov)

Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. (springer.com)

The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020. (bvsalud.org)

Release 142, produced in June 2004, contained over 40.3 billion nucleotide bases in more than 35.5 million sequences. (iospress.nl)
These sequences are composed of chemical building blocks known as nucleotide bases. (cdc.gov)
Determining the order of bases-"genomic sequencing" or simply, "sequencing"-is a core AMD technology. (cdc.gov)
The library is loaded into a sequencer, which will identify the nucleotide bases in the DNA fragments. (cdc.gov)

Anatomy5

Organisms11

Diseases3

Chemicals and Drugs54

Analytical, Diagnostic and Therapeutic Techniques and Equipment70

Phenomena and Processes90

Disciplines and Occupations11

Technology, Industry, Agriculture6

Information Science28

Health Care10

Geographicals1

Bioinformatics17

Genomes8

Genome sequences5

Humans4

Single nucleotide p1

Sanger3

International Nucleotide Se1

SNPs1

Genomics2

Phylogenetic4

Exome Sequencing7

Mutations6

Protein8

NCBI4

Genetic variation2

Next generation13

Data29

Variants4

Analyses2

Clinical1

Genes4

Reads3

Organism1

Investigate1

Centers1

Samples4

Analysis6

Biological3

GenBank3

Transcriptional2

Produces1

Fungal3

Archaeal1

Alleles4

Technologies3

Similarity1

Rare disorders1

Functional1

Publicly1

Mutation1

Platforms2

Virome2

Microbiomes1

Characterize1

Bases4