Frequencies alignment sequence analysis rna. Medical search. Frequent questions

A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. (biomedcentral.com)
WormTSS is a comprehensive collection of TSSs for trans-spliced genes generated from the sequencing of Illumina reads from pre-trans-splicing 5'-ends that were captured using a modified 5'-SAGE procedure. (xerial.org)

FastQC is a quality control tool for high-throughput sequence data (Babraham Institute) and is developed in Java. (wikipedia.org)
Kraken: A set of tools for quality control and analysis of high-throughput sequence data. (wikipedia.org)
Different studies based on computational analysis on both expressed sequence tags and high-throughput RNA sequencing provide an estimate of the frequency of these events. (biomedcentral.com)
Recently, deep sequencing of the transcriptome using high-throughput RNA sequencing (RNAseq) increased this estimate showing that more that 60% of intron-containing genes in Arabidopsis are alternatively spliced [ 12 ]. (biomedcentral.com)
Prepared libraries are sequenced on Illumina ® NovaSeq™ to enable high throughput, rapid, and deep sequencing for each cell. (q2labsolutions.com)
Scasa, an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. (ne.jp)
Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. (peerj.com)
The only earlier investigation relating to this matter was performed by our research group, which involved the identification of differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing [ 14 ]. (biomedcentral.com)

This data was also compared to whole-exome sequencing data from ten individuals. (biomedcentral.com)
When comparing the design flexibility, performance, and cost of the targeted enrichment methods to whole-exome sequencing, the RNA-bait hybridization capture enrichment gene panel offers the better solution for interrogating the aortopathy genes in a clinical laboratory setting. (biomedcentral.com)
Exome sequencing is a laboratory test designed to identify and analyze the sequence of all protein-coding nuclear genes in the genome. (nih.gov)
The diagnostic utility of exome sequencing has consistently been 20%-30% (i.e., a diagnosis is identified in 20%-30% of individuals who were previously undiagnosed but had features suggestive of a genetic condition) [ Gahl et al 2012 , Lazaridis et al 2016 ]. (nih.gov)
For the PUCH cohort, we performed HLA genotyping by whole exome sequencing (WES) analysis on the peripheral blood samples from all patients. (biomedcentral.com)

RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. (wikipedia.org)
Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. (nature.com)
PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)

The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. (wikipedia.org)
The data analysis included with the purchase of the QIAseq Immune Repertoire T-cell receptor panels includes an online portal that seamlessly integrates with Illumina BaseSpace and provides primary read mapping, UMI demultiplexing and reports on sequencing performance, TCR chain usage, CDR3 peptide sequence and length distributions, together with rarefaction and V/D/J usage heat maps. (qiagen.com)
Enriched samples were barcoded, pooled, and sequenced on the Illumina HiSeq2000 platform. (biomedcentral.com)
Second, you can use IDT rhAmpSeq technology with Illumina sequencing platforms to generate multiplexed amplicons on a per-sample basis to investigate multiple on- and off-target sites in a single reaction. (idtdna.com)

The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. (peerj.com)
To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here. (biomedcentral.com)
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. (kb.se)
Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the predicted target genes were involved in various regulatory processes, such as signal transduction mechanisms, inorganic ion transport and metabolism, defense mechanisms, translation, posttranslational modifications, energy production and conversion, and glycerolipid metabolism. (biomedcentral.com)

Currently, the detection of single nucleotide variants (SNV) from single-cell RNA sequencing data is usually performed on the pooled sequencing reads across all cells in a sample. (georgetown.edu)
The cellular barcode-stratified analysis is enriched for low (cellular) frequency variants, representing cellular heterogeneity and potential somatic mutations, which are typically under-reported in pooled scRNA-Seq analyses. (georgetown.edu)
Finally, we explored the relationship between cell types and the cell-specific observation of transcripts with expressed variants - finding a significant improvement in expressed SNV discovery in minority cell-types as compared to the pooled analysis strategy. (georgetown.edu)
However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
Variants of the HLA genes can possibly shape the sequence repertoire of neopeptides presented and influence the T cell receptor (TCR) repertoire during their continuous interaction [ 11 ]. (biomedcentral.com)
Authors are encouraged to attempt these aneuploid analyses when reporting scRNA-seq data, much like copy-number variants are commonly reported in bulk genome sequencing data. (techscience.com)
Only the non-synonymous SNPs (nsSNPs), also called as missense variants are particularly important as they result to changes in the translated amino acid residue sequence. (springeropen.com)

RainDance emulsion PCR and SureSelect RNA-bait hybridization capture enrichment methods were directly compared by enriching DNA from eight samples. (biomedcentral.com)
Read depth was greater and less variable among samples that had been enriched using the RNA-bait hybridization capture enrichment method. (biomedcentral.com)
In addition, samples enriched by hybridization capture had fewer exons with mean coverage less than 10, reducing the need for followup Sanger sequencing. (biomedcentral.com)
NGS can be used to evaluate the sequence of either the entire genome ( whole genome sequencing , WGS) or a specific region of interest by targeted enrichment techniques such as hybridization capture and amplicon sequencing . (idtdna.com)

Quality assessment of raw data is the first step of the bioinformatics pipeline of RNA-Seq. (wikipedia.org)
We recently demonstrated the feasibility of using unaligned rRNA sequences as barcodes based on a composition vector (CV) approach without sequence alignment ( Bioinformatics 22:1690). (biomedcentral.com)
The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. (hindawi.com)
In bioinformatics, the sequence alignment has become one of the most important issues. (hindawi.com)

To detect mutations in the BCR-ABL1 transcript we developed an assay based on the Pacific Biosciences (PacBio) sequencing technology, which allows for single-molecule long-read sequencing of BCR-ABL1 fusion transcript molecules. (biomedcentral.com)
The PacBio sequencing successfully identified all mutations seen by standard methods. (biomedcentral.com)
Importantly, we identified several mutations that escaped detection by the clinical routine analysis. (biomedcentral.com)
Due to the long reads afforded by PacBio sequencing, compound mutations present in the same molecule were readily distinguished from independent alterations arising in different molecules. (biomedcentral.com)
In summary the PacBio sequencing assay can be applied to detect BCR-ABL1 resistance mutations in both diagnostic and follow-up CML patient samples using a simple protocol applicable to routine diagnosis. (biomedcentral.com)
Personal genome analysis involves massive amount of data analysis: genome sequence alignment, SNP calls, finding desease-related mutations, etc. (xerial.org)
However, since post-zygotically occurring SNVs only exist in a small proportion of cells, the VAF of these mutations is usually so low in pooled scRNA-sequencing data that it does not reach the VAF threshold required by SNV discovery software designed for genomic NGS data. (georgetown.edu)
Targeted next-generation sequencing (NGS) technology detects specific mutations that can provide treatment opportunities for colorectal cancer (CRC) patients. (preprints.org)
DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. (kb.se)
These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. (kb.se)
NGS assays targeted to a panel of genomic regions associated with known pathogenic mutations offer several advantages over traditional sequencing methods, including lower cost and rapid assessment of many regions. (biomedcentral.com)
This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)

While NGS offers a promising alternative to Sanger sequencing, the clinical utility of NGS methods depends on the ability to accurately isolate or amplify the genomic regions of interest. (biomedcentral.com)
We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. (biorxiv.org)
However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. (biomedcentral.com)
An additional advantage of amplicon sequencing is the ability to evaluate multiple genomic targets at a time-this can happen on two levels. (idtdna.com)

HTSeq The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run. (wikipedia.org)
QC-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. (wikipedia.org)
qrqc Quickly scans reads and gathers statistics on base and quality frequencies, read length, and frequent sequences. (wikipedia.org)
For data analysis, UMIs and Raw Reads are used to ensure high precision around each clonotype sequence identified. (qiagen.com)
Coupled with SCExecute, a tool for barcode-stratified analysis of scRNA-Seq data, the algorithm substantially reduces the work carried out by SNV discovery tools applied to the relatively sparse barcode-stratified aligned reads. (georgetown.edu)
https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1.full.pdf a new algorithm for aligning both reads in a pair simultaneously by fuzzily intersecting the sets of candidate alignment locations for each read. (ne.jp)
An average of 7 million reads were generated with approximately 21,526 genes mapped in each sample post-inoculation at 6 h (6 HPI) and 6 days (6 DPI) using RNA-sequencing technology. (frontiersin.org)
Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. (biomedcentral.com)
Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)

Today, various assays including Sanger sequencing and quantitative RT-PCR are routinely applied for BCR-ABL1 mutation detection. (biomedcentral.com)
While Sanger sequencing has limited sensitivity, real time reverse transcription PCR requires mutation specific panels with separate standard curves and variable sensitivity. (biomedcentral.com)
However, comprehensive sequencing of the many genes involved is often impractical with traditional Sanger methods. (biomedcentral.com)
However, due to their limitations, the traditional techniques were replaced by molecular techniques such as polymerase chain reaction (PCR) and DNA sequencing (Sanger method) [ 1 ]. (biomedcentral.com)

Isolation and Whole-Genome Sequencing of Environmental Campylobacter. (cdc.gov)
Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing. (cdc.gov)
Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. (cdc.gov)

Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. (plos.org)

RSeQC analyzes diverse aspects of RNA-Seq experiments: sequence quality, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. (wikipedia.org)
Incorporate cell surface protein detection and antigen specificity analysis in conjunction with gene expression and immune repertoire profiling with our surface protein profiling assay. (q2labsolutions.com)

Single cell sequencing is a next-generation sequencing method enabling in-depth characterization of biomolecules by uncovering genetic expression at single cell resolution. (q2labsolutions.com)

Barcode-stratified analysis of scRNA-Seq data using SNV discovery software identifies many more SNVs than the same to tools applied to pooled scRNA-Seq or bulk RNA-Seq alignments. (georgetown.edu)
Unlike the analysis of pooled scRNA-Seq data, barcode-stratified analysis of scRNA-Seq data enables cell-specific observations of expressed SNVs across cells and cell-types. (georgetown.edu)
Unfortunately, the barcode-stratified SNV discovery analysis of scRNA-Seq data is time-consuming. (georgetown.edu)
In the second part of the project, we analyzed the pooled scRNA-Seq data to study SNVs observed only by the barcode-stratified analysis strategy. (georgetown.edu)
Intuitive "eyeball" calls are uncommon in bulk RNA-seq or DNA-seq determination of aneuploidy and CNAs, so it is unsurprising that a simple stacking of read counts is insufficient for quality inference of aneuploidy in scRNA-seq data. (techscience.com)

Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
HuCaT uses an algorithm based on number of matching queries, k-mers are used to calculate the actual matching nucleic acid k-mers (short substrings of DNA [n 9 nt in number of nucleotide sequence matches for type assignment using the HuCaT]) to build alignments between query and reference sequences. (cdc.gov)
Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples. (cdc.gov)

The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. (biomedcentral.com)
Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples. (biomedcentral.com)
Currently, the diagnostic methods used to detect viruses in stool samples are sequence-dependent molecular amplification techniques such as PCR, which cannot identify a pool of viruses and completely new viruses in clinical samples. (biomedcentral.com)
The family Caliciviridae consists of a genetically diverse group of typing of norovirus, short nucleotide regions at the 5'-end of the capsid single-stranded RNA viruses that can be divided into 10 genera [ 1 ]. (cdc.gov)
BLAST algorithm against a set of reference sequences followed by notypes [6 ] with viruses in GI, GII, GVIII and GIX infecting humans. (cdc.gov)

6 A partial VP1 sequence was then obtained by amplification and sequencing of a 375bp region. (who.int)

NGS QC Toolkit A toolkit for the quality control (QC) of next generation sequencing (NGS) data. (wikipedia.org)
PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. (wikipedia.org)
The Department of Biotechnology (DBT), Government of India, funded this work under the DBT-NER Twinning program "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" (Grant ID BT/325/NE/TBP/2012 dated August 07, 2014). (plos.org)
Here, using Next Generation Sequencing we identified a novel gene fusion event between DAXX and the kinesin motor protein, KIFC3, leading to the translation of a chimeric DAXX-KIFC3 fusion protein. (oncotarget.com)
In this setting next generation sequencing (NGS) offers several advantages over traditional molecular techniques. (biomedcentral.com)
Prior to the development of massively parallel sequencing (also known as next-generation sequencing ), the only cost-effective way to test more than one gene was serial single-gene testing (i.e., complete testing of one gene that might account for the phenotype before proceeding to testing of the next gene) ‒ an expensive and time-consuming approach with a potentially low yield. (nih.gov)
Aneuploidy, the loss or gain of chromosome arms, appears less prevalent in normal tissue in these clonal mutant next-generation sequencing analyses. (techscience.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)
Next generation sequencing (NGS) is the recommended method for full investigation of CRISPR edits. (idtdna.com)
Next generation sequencing (NGS) is the gold standard for analyzing CRISPR edits and is used for 1) unbiased identification and nomination of off-target sites across the genome and 2) accurate evaluation of CRISPR editing events. (idtdna.com)
Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. (cdc.gov)
Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus. (cdc.gov)

CRISPR applications typically utilize amplicon sequencing, which makes more economical use of sequencing capacity compared to WGS. (idtdna.com)
The IDT rhAmpSeq CRISPR Analysis System is based on amplicon sequencing. (idtdna.com)
Amplicon sequencing with NGS can identify and quantify the frequency of the indels that result from non-homologous end joining (NHEJ) following introduction of CRISPR-generated double-strand breaks (DSB). (idtdna.com)
Furthermore, with amplicon sequencing, you also can quantify the correct homology-directed repair (HDR) events and determine what percent of your targeted alleles successfully underwent perfect HDR, thus defining a well-resolved picture of editing events at the target site. (idtdna.com)

QC3 a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling. (wikipedia.org)
Unlike SNV discovery tools SCReadCounts output provides read-counts for monoallelic reference transcripts, distinguishing between loci with abundant transcripts, but low (cellular) frequency variant alleles, and low abundance transcripts observed in few cells. (georgetown.edu)
PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
Protein structural analysis with this amino acid variant was performed by using I-TASSER, RAMPAGE, Swiss-PdbViewer, Chimera and I-mutant. (springeropen.com)

We examined the clinically validated D. immitis P-glycoprotein 11 ( Dim Pgp-11) single nucleotide polymorphism (SNP) via MiSeq analysis in three ML-susceptible isolates (Missouri, MP3 and Yazoo) and two ML-resistant isolates (JYD-34 and Metairie), and correlated the data with previously published MiSeq results of USA laboratory-maintained D. immitis isolates. (biomedcentral.com)
Information regarding gene content, polycistronic transcription units, sequence insertion or deletion, transition or transversion, and nucleotide repeats may help resolve evolutionary relationships in the kingdom Plantae (Viridiplantae) 6 , 7 , 8 . (plos.org)
3 In 2012, the virus was assigned as EV-C105 because subsequent sequencing showed that it had only 74.7% nucleotide and 82.5% amino acid identity to EV-109, thus satisfying the criteria for assignment of a new enterovirus serotype. (who.int)
9 The sequence was compared to known VP1 sequences in GenBank using tblastx (which searches a translated nucleotide database using a translated nucleotide query). (who.int)

mRIN - Assessing mRNA integrity directly from RNA-Seq data. (wikipedia.org)
Binding of a miRNA to a complementary sequence in a target mRNA is mediated by Argonaute proteins leading to degradation of the mRNA or translational inhibition, thereby lowering protein levels in cells [ 7 ]. (researchsquare.com)
In another study, resistin mRNA was not related to insulin resistance when using RNA isolated from cultured adipocytes ( 10 ) but was upregulated by acute hyperglycemia in various mouse adipose depots ( 11 ). (diabetesjournals.org)

We report our analysis of MyoD1 and MyoD2 protein sequences from 54 teleost species, and show that O. alcalica , along with some other teleosts, include a polyserine repeat between the amino terminal transactivation domains (TAD) and the cysteine-histidine rich region (H/C) in MyoD1. (mdpi.com)
However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)

Forty-nine isolates of Trichoderma from the Brazilian Midwest were evaluated for their antagonistic activity in vitro against Sclerotinia sclerotiorum (causal agent of white mold), which were then identified based on their nuclear ribosomal ITS sequences. (scielo.br)

Profile up to 10,000 cells per sample with our single cell RNA sequencing assay. (q2labsolutions.com)
Our assay acquires single cell resolution by partitioning individual cells into nano-liter gel beads where they undergo reverse transcription and cellular barcoding followed by library preparation and sequencing. (q2labsolutions.com)

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. (wikipedia.org)
Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. (nature.com)
The level of the expression of the Dim Pgp-11 messenger RNA transcript was analyzed by droplet digital PCR (ddPCR) and compared in the USA laboratory-maintained isolates, namely the ML-susceptible Missouri and Berkeley isolates, the putative ML-susceptible Georgia III and Big Head isolates and the ML-resistant isolate JYD-34. (biomedcentral.com)
We calculated and compared allele expression for SNVs from both analysis strategies. (georgetown.edu)
Differential expression analysis demonstrated that the yoga intervention induced increased expression of antisense genes, some of which serve as antisense to known pain genes. (biomedcentral.com)
The protocol was found to be highly feasible and acceptable to participants, and preliminary analyses suggest a possible mechanism of action of yoga on pain by increasing self-efficacy and emotion regulation as well as through changes in gene expression and DNA methylation profiles. (biomedcentral.com)
Small noncoding RNAs called microRNAs (miRNA) negatively regulate gene expression by sequence-specific targeting of protein-coding transcripts [ 6 ]. (researchsquare.com)
Use fresh frozen tissue to faithfully capture RNA expression by circumventing transcriptional changes induced by traditional dissociation. (q2labsolutions.com)
We performed differential expression analysis using EdgeR and DESeq2 and examined Gene Ontologies to identify candidates potentially involved in this plasticity. (biomedcentral.com)
qRT-PCR analysis of the expression level of 13 predicted target genes and their corresponding miRNAs revealed that there was no obvious negative regulatory relationship between miRNAs and their target genes. (biomedcentral.com)
Stacked bar graphs showing different patterns of enriched spatial expression based on RNA-seq of dissected gastrula tissues (Blitz et al. (xenbase.org)
Disrupted expression in sox17 -MOs is rescued by co-injection of mouse (m) Sox17 RNA. (xenbase.org)
This resource, combining a unique new dataset and novel application of analysis methods to multiple relevant datasets, identifies numerous potential drug targets for manipulating circuit function, reveals neuron subtype-specific roles for disease-linked genes, and is useful for understanding gene expression changes observed in human patient brains. (jneurosci.org)
We used a genome-wide analysis which not only examined differential gene expression levels but could also detect differences in splice isoform usage. (jneurosci.org)

It has advantages over conventional bulk sequencing in its ability to detect rare cell types, uncover tumor heterogeneity, trace lineages, discover drug-resistant cell populations, and characterize complex cell populations such as immune cells in peripheral blood. (q2labsolutions.com)

11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)
or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
A greater awareness of EV-C105 may help to detect this virus with increased frequency and to find out more about the pathogenic role and disease association of this particular genotype. (who.int)

These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. (kb.se)
Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. (kb.se)

RNA from 22 FIPVs collected from 11 cats who had feline infectious peritonitis was extracted, purified, and reverse-transcribed into cDNA. (cdc.gov)
The QIAseq Immune Repertoire RNA Library Kit relies on a highly efficient, TCR-specific cDNA synthesis reaction, ligation of sample index adapters containing UMIs and TCR gene-specific primer enrichment for sensitive TCR clonotype and diversity assessment. (qiagen.com)
cDNA was generated from total RNA and a 1,6 kb fragment encompassing the BCR-ABL1 transcript was amplified using long range PCR. (biomedcentral.com)

These data highlight a potentially unrecognized mechanism of DAXX inactivation in ALT positive osteosarcoma and provide rationale for thorough and comprehensive analyses of ATRX/DAXX/H3.3 proteins in ALT positive cancers. (oncotarget.com)
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. (kb.se)

The clinical significance of splice isoforms remains to be elucidated, mainly because their detection has until recently required time consuming cloning steps prior to sequencing. (biomedcentral.com)
This recognition comes as ultra-deep sequencing technologies coupled with error-reducing sequencing techniques have enabled the detection of mutant cells occupying less than one percent of an examined tissue sample ( Martincorena, 2019 ). (techscience.com)

Sequencing of the spike gene was performed in a region surrounding the S1/S2 cleavage site. (cdc.gov)

This ensures sensitive, accurate and unbiased quantification of the number of TCR transcripts captured and sequenced. (qiagen.com)
Sequencing as well as functional studies using antisense oligonucleotides, indicate important roles for microRNAs during the development of epilepsy through targeting transcripts involved in neuronal structure, gliosis and inflammation. (researchsquare.com)

We can meet your sequencing needs with our extensive services spanning the clinical research continuum combined with our global laboratory network and expert support team. (q2labsolutions.com)
Due to the overlapping phenotypes presented by these disorders genetic sequencing is often required for accurate diagnosis and appropriate clinical intervention. (biomedcentral.com)
In the past ten years, improvements in massively parallel sequencing techniques have led to the development and widespread clinical use of multigene panels, which allow simultaneous testing of two to more than 150 genes. (nih.gov)
These include genes selected by a clinician for analysis by clinical sequencing. (nih.gov)
Using an initial 600-mg linezolid dose daily adjusted by therapeutic drug monitoring and careful clinical and laboratory monitoring for adverse effects, supportive care, and expert consultation throughout BPaL treatment, 3 patients (4.4%) with hematologic toxicity and 4 (5.9%) with neurotoxicity required a change in linezolid dose or frequency. (cdc.gov)

Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). (plos.org)
Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. (cdc.gov)
HuCaT tool assigned genotypes to all queries with 100 % accuracy and was much faster (17 s) than BLAST (150 s) or phylogenetic analyses approaches. (cdc.gov)
Noroviruses are associated with an compared to an established set of reference sequences to determine estimated 70,000-200,000 deaths annually [2,3 ] while sapoviruses genotypes and polymerase types based on phylogenetic clustering, or by primarily cause sporadic AGE in young children although outbreaks in employing NCBI BLAST web service. (cdc.gov)

The rhAmpSeq CRISPR Analysis System also includes an advanced but accessible cloud-based data analysis pipeline for quantification of on- and off-target edits. (idtdna.com)

1998 ). The MBL2 gene is composed of 7461 bases and lies between the regions 52765380 to 52772841 bp of chromosome no. 10 (NCBI reference sequence number NC_000010.11). (springeropen.com)

These studies present evidence that an HLA-I genotype with two alleles with higher sequence divergence, known as the HLA-I evolutionary divergence (HED), may enable the presentation of more diverse immunopeptidomes and hence facilitate subsequent T cell recognition and the adaptive immune response. (biomedcentral.com)

We analyzed the mutation frequencies of common actionable genes and their association with clinicopathological characteristics and oncologic outcomes using targeted NGS. (preprints.org)

Single-cell sequencing data has transformed the understanding of biological heterogeneity. (techscience.com)

Online analysis through the Typical HTML Report. V-J usage heatmaps for a single sample are shown. Jurkat RNA was spiked into normal human PBMC RNA at a dilution of 1:10,000 (800 Jurkat cells in 8,000,000 PBMCs). The heatmaps allow for easy identification of enriched clonotypes across the sample. Here, we see the major clonotype of the Jurkat cell, as well as the diversity of the PBMC background. "> GeneGlobe Data Analysis Center provides key sequencing QC metrics, as well as the frequency and identity of each clonotype sequenced. (qiagen.com)
Over 10,000 full-length BCR-ABL1 sequences were obtained for all samples studied. (biomedcentral.com)

Often, is necessary to filter data, removing low quality sequences or bases (trimming), adapters, contaminations, overrepresented sequences or correcting errors to assure a coherent final result. (wikipedia.org)
NGSQC: cross-platform quality analysis pipeline for deep sequencing data. (wikipedia.org)
It also includes few other tools, which are helpful in NGS data quality control and analysis. (wikipedia.org)
It is particular designed for 454/Roche data, but can also be used for other types of sequence. (wikipedia.org)
We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. (biomedcentral.com)
Characterisation of the ageing of plasma-deposited polymer films: Global analysis of X-ray photoelectron spectroscopy data. (tradingsignalsforex.com)
Silk supports running these complex data analysis pipeline in a cluster machine. (xerial.org)
Our data provides an enabling resource for both experimental and theoretical analysis of gene structure and function in C. elegans . (xerial.org)
Therefore, a new workflow has been developed for detecting SNVs in scRNA-sequencing data stratifying scRNA-sequencing data by celluar barcodes. (georgetown.edu)
Data on subjective pain characteristics, quantitative sensory testing, and blood for analysis of differentially expressed genes and CpG methylation was collected prior to the start of the intervention and at study completion. (biomedcentral.com)
The funders had no role in the study design, the data collection and analysis, the decision to publish, or the preparation of the manuscript. (plos.org)
Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. (biomedcentral.com)
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. (kb.se)
These data have been further integrated and augmented by a number of evolutionary and computational analyses. (kb.se)
This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. (deepdyve.com)
A total of 122.33 Mb of raw data was obtained from degradome sequencing analysis of YC05-179 (smut-resistant) and ROC22 (smut-susceptible) after inoculation. (biomedcentral.com)
Bioinformatic analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scRNA-seq gene counts. (techscience.com)
In this viewpoint, we direct investigators to select scRNA-seq CNA data analysis tools. (techscience.com)
Specialized software has thus been developed to appropriately handle RNA-seq data in the context of CNA determination. (techscience.com)
2 Due to a lack of sequence data this virus was initially identified as Enterovirus 109 (EV-109). (who.int)
Threats to timely sharing of pathogen sequence data. (cdc.gov)

In particular, the RNA interference (RNAi) pathways are of notable significance for the control of viral infections. (mdpi.com)
1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. (genominfo.org)

QIAseq Immune Repertoire RNA Library Kits are intended for molecular biology applications. (qiagen.com)
The QIAseq Immune Repertoire RNA Library Kits use Unique Molecular Indices (UMI) with gene-specific primers to target specific RNAs for NGS sequencing. (qiagen.com)
By using UMIs, the QIAseq Immune Repertoire RNA Library Kit Panel eliminates PCR duplicates and minimizes artifacts that may arise during the library preparation process or during the sequencing run. (qiagen.com)
Using TCR alpha and beta repertoire sequencing for T-cell subsets, as well as single-cell RNAseq and TCRseq, we track the concentrations and phenotypes of individual T-cell clones in response to primary and secondary yellow fever immunization - the model for acute infection in humans - showing their large diversity. (elifesciences.org)

Molecular dating estimates and biogeographic analyses indicate that the early diversification of this clade happened in the Western Ghats and Sri Lanka during the Late Oligocene to Early Miocene. (biomedcentral.com)
A comprehensive analysis of the molecular markers for CRC can provide insights into the mechanisms underlying disease progression and help optimize a personalized therapy. (preprints.org)

The human exome includes all coding nuclear DNA sequences, approximately 180,000 exons that are transcribed into mature RNA. (nih.gov)

Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. (biomedcentral.com)
Tumor tissues from 76 patients were subjected to WES analysis and immune oncology-related RNA profiling. (biomedcentral.com)

RNA-SeQC is a tool with application in experiment design, process optimization and quality control before computational analysis. (wikipedia.org)

The first application of metagenomics study in virus discovery was the analysis of virus particles in soil samples from marine sites in San Diego [ 9 ]. (biomedcentral.com)

We explore techniques to speed up the analysis and further study the characteristics of observed SNVs to improve our understanding of single-cell expressed SNVs. (georgetown.edu)
Request a quote today to discover how single cell sequencing with Q 2 Solutions can advance your research. (q2labsolutions.com)
While many flavors of single-cell sequencing have been developed, single-cell RNA sequencing (scRNA-seq) is currently the most prolific form in published literature. (techscience.com)
Given that aneuploidy is (a) known to contribute to cell biology and (b) is present at some detectable level in many cell types, it is valuable for single-cell sequencing studies to include aneuploidy information in their analyses. (techscience.com)

When the biologists get an unknown sequence, in general they would compare this unknown sequence (denoted as query sequence) with the known database of sequences (denoted as database sequences) to find the similarity scores and then identify the evolutionary relationships among them. (hindawi.com)
Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. (kb.se)

Each unique panel is carefully designed and laboratory-verified for sequencing performance with a UMI-aware alignment software for maximum sequencing performance and accurate results. (qiagen.com)
Results for each gene on the custom multigene panel are reported to the ordering clinician, whereas the results from the remaining genes sequenced (but not requested by the clinician) are not analyzed or included in the final laboratory report. (nih.gov)

Needleman and Wunsch [ 1 ] proposed a dynamic programming method (abbreviated to NW algorithm) to solve the global alignment problem between two sequences in 1970. (hindawi.com)

Traditionally, sequences are gastroenteritis (AGE) in humans. (cdc.gov)

The short-term solution is to divide the large barcode dataset into several "sub-projects" with a size limit of 5,000 specimens each for analysis [ 7 ]. (biomedcentral.com)
Together they account for 44 % (284/650) of all off-target sequences in our dataset and 71 % (84/119) of the off-targets with five or more mismatches. (biomedcentral.com)

The telomerase holoenzyme promotes telomere elongation by using the RNA component TERC as a template for reverse transcription at telomere ends. (oncotarget.com)
Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. (kb.se)
7 Enteroviral RNA was detected using real-time reverse transcription polymerase chain reaction. (who.int)

The goal of BOLD is to generate a "taxon ID tree" based on a neighbour-joining (NJ) algorithm for every query sequence for easy identification. (biomedcentral.com)
We found the algorithm to focus SNV discovery tools to regions with sufficient depth was extremely effective in speeding up the analysis, with little to no change in the SNVs observed. (georgetown.edu)
The Smith-Waterman (abbreviated to SW) algorithm, which was proposed by Smith and Waterman [ 2 ] in 1981, is designed to find the optimal local alignment, and it is enhanced by Gotoh [ 3 ] in 1982. (hindawi.com)
Web-based to query sequences using a k-mer (DNA substring) based algorithm. (cdc.gov)

Though the NW and SW algorithms guarantee the maximal sensitivity for the alignment, the cost is still expensive, especially for the computation time. (hindawi.com)

We also found, as expected, more SNVs present only in a small subset of cells, from the barcode-stratified scRNA-Seq analysis compared with the pooled scRNA-Seq analysis, as well as more novel SNVs, missing from dbSNP. (georgetown.edu)

ALT is a recombination-based mechanism where one telomere uses other chromosomal, or extrachromosomal, telomeric DNA sequences as a template for telomere elongation. (oncotarget.com)

Anatomy7

Organisms13

Diseases1

Chemicals and Drugs85

Analytical, Diagnostic and Therapeutic Techniques and Equipment38

Phenomena and Processes102

Disciplines and Occupations3

Information Science24

Health Care10

Geographicals1

Spliced genes2

High-throughput8

Exome Sequencing5

Transcriptome3

Illumina4

Genomes4

Variants7

Hybridization capture4

Bioinformatics4

Mutations12

Genomic4

Reads9

Sanger4

Whole genome3

Genomics1

Specificity2

Uncovering genetic1

ScRNA-Seq data5

Nucleic acid3

Viruses5

Amplification1

Next generation13

Amplicon4

Variant4

Nucleotide4

MRNA3

Protein sequences2

Ribosomal1

Assay2

Expression14

Bulk1

Pathogenic3

Drosophila2

CDNA3

Comprehensive analyses2

Detection2

Cleavage1

Transcripts2

Clinical5

Phylogenetic4

Quantification1

Chromosome1

Genotype1

Actionable1

Heterogeneity1

10,0002

Data21

Pathways2

Repertoire4

Molecular2

Exons1

Tissues2

Computational1

Metagenomics1

Single-cell4

Evolutionary2

Results2

19701

Gastroenteritis1

Dataset2

Transcription3

Algorithm4

Sensitivity1

Cells1

Chromosomal1