Consensus sequence. Medical search. Frequent questions

By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes, and epigenetic assays for genetic disorders. (nih.gov)
One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). (warwick.ac.uk)
Results: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. (warwick.ac.uk)
Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. (warwick.ac.uk)
Since the completion of the human genome project in 2003, extraordinary progress has been made in genome sequencing technologies, which has led to a decreased cost per megabase and an increase in the number and diversity of sequenced genomes. (nature.com)
These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease. (nature.com)
In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. (niema.net)
Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
We analyzed whole-genome sequencing data from 2,511 individuals in the Pan-Cancer Analysis of Whole Genomes (PCAWG) study as well as 489 individuals from four prospective cohorts and found distinct regional mutation type-specific frequencies in tissue and cell-free DNA from patients with cancer that were associated with replication timing and other chromatin features. (nature.com)
Sequence alterations are abundant in cancer genomes but the proportion of fragments in cell-free DNA (cfDNA) that harbor tumor-specific (somatic) mutations is often low 8 , 9 , making it difficult to detect bona fide variants amidst background noise from sequence changes introduced in library construction and sequencing. (nature.com)
While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. (researchgate.net)

It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. (seqanswers.com)
When available, the information provided by whole-genome sequencing projects provides an entry into an understanding of genome structure and evolution and gene discovery, and function. (biomedcentral.com)
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)
While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. (frontiersin.org)
Compared to whole genome sequencing (WGS), exome sequencing covers only the 1% of the genome that is translated into protein, greatly reducing the technical burden of data collection and analysis. (frontiersin.org)
performed the first whole-genome sequencing study on AML cells collected from a single patient. (frontiersin.org)

It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. (wikipedia.org)

Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (biomedcentral.com)
Our Capacity-Building in Genomic Surveillance and Epidemiology program aims to build genomic surveillance using portable and affordable sequencing such as the Oxford Nanopore Technologies MinION platform and bioinformatics and phylodynamics modeling capabilities to enable a more efficient response to disease outbreaks. (nih.gov)
In Australia, integration of genomic sequencing METHODS into the response to COVID-19 has al owed clusters and outbreaks to be identified and transmission chains to COVID-19 cases notified to the Tasmanian Department of be rapidly detected. (who.int)

The Committee concluded that full-length genome sequences from additional variola major and minor strains, particularly Congo 70 and Somalia 77, should be determined and that additional clone libraries from selected strains should be prepared. (who.int)

The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. (nih.gov)
In this context the ACMG convened a workgroup in 2013 comprising representatives from the ACMG, the Association for Molecular Pathology (AMP), and the College of American Pathologists to revisit and revise the standards and guidelines for the interpretation of sequence variants. (nih.gov)
1) You can find out variants by a reference sequence and an assembly. (ugene.net)
The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results. (wustl.edu)
The plurality consensus sequence is very useful when used with the BAM file to look at minor variants, since the most frequent allele will appear in the reference. (cdc.gov)
F1 contains 401 de novo synonymous benign variants within the consensus coding sequence (CCDS) and identified from individuals not ascertained for any specific disorder. (lu.se)

In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. (wikipedia.org)
Bioinformatics tools are able to calculate and visualize consensus sequences. (wikipedia.org)
This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). (warwick.ac.uk)
However, storage of the raw sequence data can become prohibitively large, and computing consensus genome from sequence data can be slow and requires bioinformatics expertise. (niema.net)
While the reduction in the cost of WGS is making sequencing more affordable in lower- and middle-income countries (LMICs), public health laboratories in these countries seldom have access to bioinformaticians and system support engineers adept at using the Linux command line and complex bioinformatics software. (researchgate.net)

1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. (nih.gov)

Position-specific scoring matrix Regular expression - denoting multiple sequences of symbols in formal language theory Sequence motif Sequence logo Pierce, Benjamin A. 2002. (wikipedia.org)
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
This proline-rich sequence, referred to as the PY motif, is known to be a site of binding by proteins bearing a WW domain. (nih.gov)
In the nearest neighbor model the free energy change for each motif depends on the sequence of the motif and of its closest base-pairs. (wikipedia.org)
Support for various forms of sequence motif matrices. (biopython.org)

using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. (biomedcentral.com)
Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (biomedcentral.com)
Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
Regions of the L. killicki ( L. tropica ) and L. major genes sequences were scanned using BLAST program and subsequently compared using appropriate bioinformatic tools Chromas and MEGA. (who.int)

A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several times in the genome and is thought to play the same role in its different locations. (wikipedia.org)
On the contrary, mutations that destroy conserved nucleotides in the consensus sequence are known as down mutations. (wikipedia.org)
[6] For longer molecules, the number of possible secondary structures is huge: a sequence of 100 nucleotides has more than 10 25 possible secondary structures. (wikipedia.org)

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)
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)
Sequencing was conducted by tiled amplicon polymerase chain reaction with ARTIC v1 or v3 primers and Illumina sequencing. (who.int)

These types of mutations down-regulate transcription since RNA polymerase can no longer bind as tightly to the core promoter sequence. (wikipedia.org)
Missense mutations altering a consensus PPPXY sequence of the alpha, beta or gamma subunits reproduced the increase in channel activity found in mutants in which the entire cytoplasmic C-termini are deleted. (nih.gov)
Several mutations in the N terminus of the G-protein-coupled receptor rhodopsin disrupt NXS/T consensus sequences for N-linked glycosylation (located at N2 and N15) and cause sector retinitis pigmentosa in which the inferior retina preferentially degenerates. (jneurosci.org)

For each input multiple alignment the workflow calculates the consensus and saves it to a fasta file, named according to the name of the input alignment. (ugene.net)
It means that the consensus will only contain characters that are the same in ALL sequences of the alignment. (ugene.net)
The workflow sample 'Extract Consensus as Sequence' can be found in the 'Alignment' section of the Workflow Designer samples. (ugene.net)
For each input alignment the workflow outputs separate sequence file with consensus in it. (ugene.net)
Optionally, if an HMM profile is provided in your module, one can use it to globally align the plurality consensus to the profile and also create an amended alignment. (cdc.gov)
will appear in main folder for the plurality alignment and also in the amended_consensus folder. (cdc.gov)
versus the amended consensus alignment. (cdc.gov)
The multiple sequence alignment of 16 subunit VII homologues showsthat Bmuccr is very hydrophilic, has a characteristic charge distribution, and has a high helical content. (researchgate.net)
I have a question about sequence alignment (i known that it isn't the subject of this forum, but i'll be very glad for any help). (salilab.org)
From a alignment, i intend to extract the consensus sequence differently. (salilab.org)
In order to create the .ali alignment file which is neccessary for the computation of the final structure prediction of my target sequence, i will need to run malign.py. (salilab.org)
First of all we proceeded to an alignment using the CLUSTAL W program to each Leishmania species and for the selected gene (cysteine protase b) (the alignment use published sequences and sequences which were sequenced in our laboratory). (who.int)

Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)

Sequence-specific, single primer amplification and detection of PCR products for identification of hepatitis viruses. (cdc.gov)
We opted for conserved sequences between species, presenting enough sequence heterogeneities to be considered for the design of species- specific LAMP primers: such primers would allow the selective amplification of the DNA targets. (who.int)
The sequences identified in the previous section of the work were used to design a combinations of 6 primers in 8 distinct regions of the target sequences for the amplification of a selection of reference DNAs belonging to the different Old World Leishmania species. (who.int)

Specific sequence motifs can function as regulatory sequences controlling biosynthesis, or as signal sequences that direct a molecule to a specific site within the cell or regulate its maturation. (wikipedia.org)

The nested PCR primers used to isolate HCV sequences were designed and manufactured within CDC. (cdc.gov)

1 denotes unique sequences. (cdc.gov)
Two approaches were developed to identify unique sequences to L. major in the first case and to L. tropica in the second. (who.int)
It is likely to identify unique sequences to L. major of this type. (who.int)

The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are variable. (wikipedia.org)

According to a procedure that has been previously validated for the identification of species - specific targets among which some fragments would fit into the second category of sequences expected. (who.int)

We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean ( Glycine max L. Merr. (biomedcentral.com)
Phylogenetic analysis of 18S rRNA gene sequences placed Tylenchus zeae n. sp. (bvsalud.org)

Transposons act in much the same manner in their identification of target sequences for transposition. (wikipedia.org)

Thus a consensus sequence is a model for a putative DNA binding site: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized sequence that represents the predominant base at each position. (wikipedia.org)
This spacer and the putative promoter 600 bp upstream from the hsa‐miR‐200c stem-loop contain six putative binding sequences for [zinc‐finger E‐box binding homeobox 1] ZEB1, two of which were restricted to ZEB factors (Z‐box 1 and 2, CAGGTA). (wikiversity.org)

Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)
Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (wikipedia.org)

CR1-type non-ltr retrotransposon :consensus sequence. (girinst.org)
COPIA3-LTR_AG is a long terminal repeat of the COPIA3_AG LTR retrotransposon - a consensus sequence. (girinst.org)

Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. (seqanswers.com)

Finally, splice sites (sequences immediately surrounding the exon-intron boundaries) can also be considered as consensus sequences. (wikipedia.org)

I asked this question at seqanswers forum and got an answer that creating the consensus sequences is possible with UGENE command line. (ugene.net)

This is a graphical representation of the consensus sequence, in which the size of a symbol is related to the frequency that a given nucleotide (or amino acid) occurs at a certain position. (wikipedia.org)
The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn. (wikipedia.org)
Each kinase will phosphorylate its substrates on amino acid patterns sharing sequence similarities, and many publications describe the consensus sequences recognized by particular kinases. (eurogentec.com)
Together, these results indicate that the structure of the rhodopsin N terminus must be maintained by an appropriate amino acid sequence surrounding N2 and may require a carbohydrate moiety at N15. (jneurosci.org)

Short-read sequencing approaches provide lower-cost, higher-accuracy data that are useful for population-level research and clinical variant discovery. (nature.com)
These include integrated long-read and short-read sequencing studies, routine clinical DNA sequencing, real-time pathogen DNA monitoring and massive population-level projects. (nature.com)
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. (wustl.edu)
First, this article summarizes the history of massively parallel next-generation sequencing (NGS) in the context of cancer genomics and reviews recent research and clinical applications. (frontiersin.org)

Consensus sequences were generated, sequences were aligned to a reference sequence and phylogenetic analysis was performed. (who.int)

Can I have an example of an UGENE command that can be used to build consensus sequences from ref.fasta and sorted.bam files? (ugene.net)

Figure 2: Sequencing by ligation methods. (nature.com)

In IGV, I can create consensus sequence for all references (one by one). (ugene.net)

where the A is call of the alternate allele in this individual and the M is actually a well-supported call of the reference sequence at this site (not sure why it is given as an ambiguity). (seqanswers.com)

By virtue of increased complexity, this shift in genetic testing has been accompanied by new challenges in sequence interpretation. (nih.gov)
the costs and error rates of long-read sequencing make it prohibitive for routine use, and ethical considerations can limit the public and private use of genetic data. (nature.com)
Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (biomedcentral.com)
The elucidation of the human genome sequence has made it potential to ascertain genetic alterations in cancers in unprecedented component. (ncbcs.org)
For example, developed and developing nations disagree on whether derivatives of genetic resources (such as genetic sequencing data) should be shared. (lu.se)

Hi, I have used BWA to map reads from ~45 individuals of my favorite species to a reference (haploid) mitochondrial DNA sequence. (seqanswers.com)
Although the morphological data of the sportive lemurs at Montagne des Français was comparable to that of Sahafary, the sportive lemur at Montagne des Français was subsequently verified as L . septentrionalis with mitochondrial DNA D-loop sequence data analyses. (bioone.org)

Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (wikipedia.org)

By contrast, long-read approaches provide read lengths that are well suited for de novo genome assembly applications and full-length isoform sequencing. (nature.com)
Some approaches maximize the number of bases sequenced in the least amount of time, generating a wealth of data that can be used to understand increasingly complex phenotypes. (nature.com)
Alternatively, other approaches now aim to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions. (nature.com)
Figure 3: Sequencing by synthesis: cyclic reversible termination approaches. (nature.com)
Figure 4: Sequencing by synthesis: single-nucleotide addition approaches. (nature.com)
Figure 5: Real-time and synthetic long-read sequencing approaches. (nature.com)
With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. (frontiersin.org)

As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move toward more complete 100% genome sequencing. (frontiersin.org)
allow proceeding to the in silico comparative genomics analysis of Leishmania DNAs and annotating the sequences identified. (who.int)

The second type of base amendment is for consensus allele quality control . (cdc.gov)
IRMA uses both the average consensus allele quality score as well as the consensus allele coverage depth. (cdc.gov)

I would presume that there are some parts of the viral sequence that mutate and diversify relatively freely (aren't constrained by the infection process). (scienceblogs.com)

This variable denotes the sequence that has been isolated for each participant. (cdc.gov)
0 denotes a consensus sequence with no quasispecies analysis. (cdc.gov)

Due length of the sequences, data is available in text files to avoid truncation. (cdc.gov)
The sequences were analyzed in silico by BLAST searching for homologies with other DNAs deposited in the local and public data bases. (who.int)

The HCV RNA was isolated and sequenced either to determine the genotype of the isolated virus or to determine the viral quasispecies diversity within an infected individual. (cdc.gov)

All the actual examples shouldn't differ from the consensus by more than a few substitutions, but counting mismatches in this way can lead to inconsistencies. (wikipedia.org)

People are developing ways to sequence the population of HIV viruses, but that creates a whole new set of difficulties: populations of HIV can change rapidly, and, if there's a response to the new patient's immune system, that too can alter frequencies of individual HIV viruses. (scienceblogs.com)

Snail-related and E2A factors bind to a consensus E-box promoter element (CANNTG), whereas ZEB factors bind to a related, but not necessarily identical sequence (CAGGTG/A), termed Z-Box. (wikiversity.org)
In some PCR reactions multiple sequences have identical nucleotide sequences, for example if five PCR products have identical sequences a 5 will be found in this column. (cdc.gov)

To eliminate that problem, we can use what's known as 50% majority consensus, where we call those bases for which only 50% of the sequences yield the same base (i.e., here we would report NCTGN), but we lose a lot of information (since CTG is invariant, that doesn't help us). (scienceblogs.com)

The 'strict' algorithm with the 'threshold' parameter set to '100%' is used by default to calculate the consensus. (ugene.net)
Also, you may select another algorithm to calculate the consensus. (ugene.net)
The algorithm of consensus extracting. (ugene.net)

The consensus coding sequences of human breast and colorectal cancers. (ncbcs.org)

2006. Sequencing for quasispecies analysis was done using the method described by Ramachandran et al. (cdc.gov)
Careful analysis of the surrounding region of a PTM is necessary when requesting the production of a PTM-specific antibody, to make sure that the sequence around the PTM will allow the antibody binding. (eurogentec.com)

Mardis, E. R. Next-generation sequencing platforms. (nature.com)

A plurality rule was chosen over majority consensus because it is more inclusive for pattern matching purposes and does not assign strict thresholds for the dominant virus phase in the sample. (cdc.gov)

In case of homologies identified with the other Leishmania species, these sequences were compared to L. major and/or L. tropica using MEGA software. (who.int)

Three of the reported splicing anomalies are due to sequence changes remote from exon/intron boundaries, described for the first time in TSC. (mdc-berlin.de)

In models that allow noiseless communication, we prove a reduction of (a suitable variant of) Broadcast to binary Consensus, that preserves the communication model and all complexity parameters such as randomness, number of rounds, communication per round, etc., while there is a loss in the success probability of the protocol. (dagstuhl.de)

Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. (warwick.ac.uk)

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. (warwick.ac.uk)
There are two major paradigms in next-generation sequencing (NGS) technology: short-read sequencing and long-read sequencing. (nature.com)
This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. (frontiersin.org)

Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as an up mutation. (wikipedia.org)
The absolute transcriptional activity of the promoter was 55‐fold higher than the activity of the spacer sequence. (wikiversity.org)

Such information is important when considering sequence-dependent enzymes such as RNA polymerase. (wikipedia.org)

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