Multiple sequence. Medical search. Frequent questions

This phenomenon was thought to be relatively rare in multiple myeloma, but a new study in Nature Medicine led by Nizar J Bahlis, MD , of the Arnie Charbonneau Cancer Institute , University of Calgary, Calgary, Canada, has found several kinds of these mutations in whole genomes sequenced from 30 patients previously exposed to these therapies. (tgen.org)
Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
COVID-19-compatible symptoms, and symptomatic HCP sequencing demonstrated that SARS-CoV-2 viral genomes were sent home per MDH and CDC guidance. (cdc.gov)
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)
they differ by 6-29 available genome sequences revealed single contig single nucleotide polymorphisms (SNPs) and share ST271 genomes that shared highest relatedness with identical serotype 3 capsular polysaccharide biosyn- 3/ST271. (cdc.gov)
In the United Kingdom, Genomics England seeks to assess the feasibility, benefits, and risks of whole genome sequencing as part of the Newborn Genomes Programme , an analysis of 100,000 newborn genomes. (medscape.com)
Although France's initiative for genomic medicine, France Génomique 2025, does not envisage a neonatal genome sequencing screening program, a team in Dijon is studying several dozen genomes to determine the medical and financial benefits of such a program, explained Geneviève. (medscape.com)

With recent availability of next-generation sequencing (NGS), it is becoming more common to pursue disease-targeted panel testing rather than traditional sequential gene-by-gene dideoxy sequencing. (molvis.org)
There are two major paradigms in next-generation sequencing (NGS) technology: short-read sequencing and long-read sequencing. (nature.com)
Mardis, E. R. Next-generation sequencing platforms. (nature.com)
The information in this article contains billing, coding or other guidelines that complement the Local Coverage Determination (LCD) for MolDX: Next Generation Sequencing for Solid Tumors L38045. (cms.gov)
Next Generation Sequencing (NGS) is one technique that can measure one or more genetic variations as a laboratory diagnostic test, such as when used as a companion in vitro diagnostic test. (cms.gov)

For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. (wikipedia.org)

When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. (wikipedia.org)

In keeping with its mission to translate genomic findings into clinical practice, TGen will open a clinical lab in 2024 that provides whole genome sequencing results for acute myeloid leukemia and multiple myeloma patients within 48 hours. (tgen.org)
Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations. (pacb.com)

ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)

Initial genetic analysis was performed on one family member with traditional Sanger single gene sequencing and/or panel-based testing, and ultimately, retinal gene-targeted NGS was required to identify the underlying cause of disease for individuals within the three families. (molvis.org)
Multiple genes contributing to the retinal dystrophy genotypes within a family were discovered using retinal gene-targeted NGS. (molvis.org)
How to take exon sequence of a gene for multiple species? (biostars.org)
I need to take exon sequence of MSTN gene of myotis davidii and then compare it with various species MSTN exon. (biostars.org)
This now enables investigation of how parameters such as clonal expansion relate to gene expression phenotypes [ 28 ], thereby providing novel insights not accessible by bulk sequencing (e.g. (nature.com)
Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies. (leibniz-lib.de)
Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. (lu.se)
Whole exome or whole genome sequencing is typically used when single gene or panel testing has not provided a diagnosis, or when the suspected condition or genetic cause is unclear. (medlineplus.gov)
Whole exome or whole genome sequencing is often more cost- and time-effective than performing multiple single gene or panel tests. (medlineplus.gov)

Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. (nih.gov)
Among the newest types of treatments for multiple myeloma are T cell immunotherapies that target specific tumor proteins. (tgen.org)
The first and most important step in studying a newly discovered protein sequence is to search protein databases for proteins that are similar or closely-related to the new protein, and then to align the new protein sequence to these proteins. (concordia.ca)
DNA, RNA sequences as well as proteins have been disclosed in patents since the 60s and a few even before that. (questel.com)

above, three of the samples were sequenced over both batches (B1 and B2), meaning that reads from the same test tube were sequenced twice. (bioconductor.org)
The issue I have is that, for those samples that were sequenced in both batches, I'm currently counting their reads as if they derived from cells from a different prep, when in fact they come from cells from the same prep. (bioconductor.org)

Obviously, pharmaceutical industry, biotech, agrochemical and seed companies produce the bulk of sequence patents. (questel.com)

A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. (wikipedia.org)
There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. (wikipedia.org)
In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. (wikipedia.org)
Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. (vu.nl)
It is therefore important to identify possible random similarity within sequence alignments in advance of model estimation and tree reconstructions. (leibniz-lib.de)
We propose an alternative method which can identify random similarity within multiple sequence alignments based on Monte Carlo resampling within a sliding window. (leibniz-lib.de)
In consequence, consensus profiles identify dominating patterns of non-random similarity or randomness within sections of multiple sequence alignments. (leibniz-lib.de)
A multiple alignments is then a collection of Alignatum objects. (github.com)

Computational algorithms are used to produce and analyse the MSAs due to the difficulty and intractability of manually processing the sequences given their biologically-relevant length. (wikipedia.org)
In spite of considerable research and efforts that have been recently deployed for improving the performance of multiple sequence alignment (MSA) algorithms, finding a highly accurate alignment between multiple protein sequences still remains a challenging problem. (concordia.ca)
This program switches between different alignment algorithms and between sequences and profiles, so I wanted to create a library that aligns any collection of objects with various algorithms using the same syntax. (github.com)
A human operator is generally better than software algorithms at judging what is an interesting low intensity monoisotopic peak, as opposed to a noise peak, and what is a reasonable identity given mass deviations and sequence coverage. (lu.se)

ProMSED can align complete set of sequences, its subset and any selected block, providing thus flexible tool for sequences analysis, visualization, edition and illustrations preparation. (bio.net)

From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (wikipedia.org)
Thus, the alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics analyses, and has been used in many applications, including sequence annotation, phylogenetic tree estimation, evolutionary analysis, secondary structure prediction and protein database search. (concordia.ca)

In particular, groups of genes on the man's Y chromosome and in his mitochondrial DNA were unlike those seen in earlier studies of ancient Romans but similar to sequences carried by some people living today on the Italian island of Sardinia. (newscientist.com)

Recent advances in single-cell sequencing enable recovery of the complete adaptive immune receptor sequences in addition to transcriptional information. (nature.com)
Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches. (lu.se)

Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. (wikipedia.org)
They also show that families with the CDKN2A 113insArg mutation have an increased risk not only of multiple melanomas and pancreatic carcinoma but also of breast cancer. (lu.se)

In this chapter, we report on high-resolution structures of single and multi RRM-RNA complexes to explain the numerous strategies used by these domains to interact specifically with a large repertoire of RNA sequences. (nih.gov)
Together, this dataset provides a resource for immunologists that can be integrated with future single-cell immune repertoire and transcriptome sequencing datasets. (nature.com)

Starting in the 90s, and the human genome project, genomic and mRNA sequences started to become more common in patents. (questel.com)

Sequencing libraries were built from purified genomic DNA using the Ion Xpress Plus gDNA library preparation protocol. (nih.gov)

A method is described for visualizing three nucleic acid sequences simultaneously by in situ hybridization using a new blue immunofluorescent label, amino methyl coumarin acetic acid (AMCA), in combination with green and red fluorescing FITC and TRITC. (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)
building blocks (nucleotides) in an individual's genetic code, a process called DNA sequencing. (medlineplus.gov)
Genetic predisposition for Multiple Myeloma. (lu.se)

Additionally, randomly similar sequences or ambiguously aligned sequence sections can negatively interfere with the estimation of substitution model parameters. (leibniz-lib.de)

In these situations, the authors typically have multiple sequencing runs of the same Cellranger-derived cDNA library. (bioconductor.org)

Subject: ANNOUNCEMENT: Protein Multiple Sequences Editor for Win 3.x/95 Dear All, With the increasing of protein sequence data, multiple alignment is one of the important techniques to understand protein structure-function organization and evolution. (bio.net)
The objectives of this thesis are to develop a novel scheme to predict indel flanking regions (IndelFRs) in a protein sequence and to develop an efficient algorithm for the alignment of multiple protein sequences incorporating the information on the predicted IndelFRs. (concordia.ca)
In the first part of the thesis, a variable-order Markov model-based scheme to predict indel flanking regions in a protein sequence for a given protein fold is proposed. (concordia.ca)

Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. (wikipedia.org)
Many laws have been created and modified over time to allow different types of biological material to be patented, such as naturally occurring sequences, modified sequences, sequences used in diagnostics, sequences from plants and many other types. (questel.com)
Biological sequence searches are different for several reasons. (questel.com)
History: Alignlib contains a collection of methods for classical biological sequence alignment. (github.com)

Short-read sequencing approaches provide lower-cost, higher-accuracy data that are useful for population-level research and clinical variant discovery. (nature.com)
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)

This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)

Repeats the closest preceding sequence number. (microsoft.com)
It started in 1999 from C code that I had created for a program called RADAR that is used to find repeats in protein sequences. (github.com)

ProMSED is an easy-to-use application for Windows 3.x/95 that performs automatic and manual multiple protein sequences alignment, alignment analysis and editing. (bio.net)
Manual alignment and sequence analysis are facilitated by using group operations and amino acid color-coding reflecting amino acid similarity in physico-chemical and mutational properties, secondary structure propensities, etc. (bio.net)
As new protein sequences are discovered on an everyday basis and protein databases continue to grow exponentially with time, analysis of protein families, understanding their evolutionary trends and detection of remote homologues have become extremely important. (concordia.ca)
Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis. (cms.gov)
Although drug sequences with ocrelizumab in first- and second-line were more cost -effective than ofatumumab, our probabilistic analysis suggests this outcome was very uncertain. (bvsalud.org)

In fact, up to 65% of relapsing multiple myeloma patients could be affected by mutations that impact targeted T cell treatments, according to the study authors, including researchers from the Translational Genomics Research Institute (TGen), part of City of Hope, and City of Hope , one of the largest c ancer research and treatment organizations in the United States. (tgen.org)
The findings could help clinicians and patients choose from among a variety of T cell therapies for multiple myeloma to find treatments that best match a patient's available tumor targets. (tgen.org)
According to Jonathan Keats, Ph.D . , Director of Bioinformatics at TGen, Scientific Director of the Judy and Bernard Briskin Center for Multiple Myeloma Research at City of Hope, and a co-author on the paper, the currently approved T cell therapies target either B cell maturation antigen (BCMA) or the GPRC5D protein on the surface of tumor cells. (tgen.org)
Keats' research is supported by the Judy and Bernard Briskin Center for Multiple Myeloma Research at City of Hope, the Multiple Myeloma Research Foundation , and the City of Hope Comprehensive Cancer Center NCI Core Grant (P30 CA 033572). (tgen.org)

A Seq field in a header, footer, annotation, or footnote doesn't affect the sequence numbering that results from Seq fields in the document text. (microsoft.com)

The method infers similarity profiles from pairwise sequence comparisons and subsequently calculates a consensus profile. (leibniz-lib.de)

These 3 pneumo- sites within the serotype 3/sequence type 271 progeny coccal isolates represent a novel recombinant sero- revealeda55.9-kbdonatedfragmentthatencompassed type 3 variant of the globally distributed, antimicro- cps3, pbp1a, andadditionalvirulencefactors. (cdc.gov)

It is shown through extensive performance evaluation that the proposed predictors are able to predict IndelFRs in the protein sequences with high values of accuracy and F1-measure. (concordia.ca)
It is also shown that if one is interested only in predicting IndelFRs in protein sequences, it would be preferable to use the proposed predictors instead of HMMER 3.0 in view of the substantially superior performance of the former. (concordia.ca)

In this report, we describe using NGS to identify multiple disease-causing mutations that contribute concurrently or independently to retinal dystrophy in three relatively small families. (molvis.org)
First, there is a common language to describe DNA/RNA and amino acid sequences, entirely independent from the native language the patent is written in. (questel.com)

I want to the replace the accession Id 'admin_1_45' similarly in following sequences to. (unix.com)

We show that multiple variations of their canonical fold can be used to adapt to different single-stranded sequences with a large range of affinities. (nih.gov)
Insertion/deletion (indel) and substitution of an amino acid are two common events that lead to the evolution of and variations in protein sequences. (concordia.ca)

Practical considerations such as the necessary cost and time required to generate and analyze each single-cell sequencing sample has been a limitation to performing large-scale experiments (i.e., with many samples). (nature.com)

If you want to use an image sequence, just select the first image, then go into shader editor, change single image to image sequence and frames to your number of frames. (stackexchange.com)
admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. (unix.com)
o A single site can be access by index s[i] (where s is Sequence instance). (bio.net)

Why patent sequence search is different? (questel.com)

but i wish to take only exon 1 sequence. (biostars.org)

I think we should store the last sequence number we knew about, and then let the timeout do the work. (samba.org)

For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. (wikipedia.org)

The function combine takes multiple sequences and creates a list in which each item is constructed from items from each input sequence, and all possible combinations are created. (activestate.com)
will give combine a list that it can loop over multiple times, creating proper results. (activestate.com)

A total of 8 radiomic features from 3 MRI sequences displayed significant differences between LGGs and HGGs. (medscimonit.com)

Thanks to Python's *args tuple packing way of handling an arbritrary number of arguments and the use of recursion, these functions don't care how many sequences are handed to them. (activestate.com)

This is doubly incorrect as (i) the same cell is artificially copied across multiple count matrices, and (ii) the sequencing depth is diluted across all the copies. (bioconductor.org)
The mitochondrial genome is a 16569 base-pair closed circular loop of double-stranded DNA found in multiple copies within the mitochondrial matrix. (medscape.com)

In C++, sequence containers are a group of template classes used to store data elements. (codeguru.com)
In essence, the array sequence container is nothing but a class representation of a C-style array data structure. (codeguru.com)
The approach has been extended to aminoacid and nucleotide data and is currently further developed to visualize total randomness among sequences of a multiple sequence alignment together with Dr. Patrick Kück and Sandra Meid, both ZFMK. (leibniz-lib.de)
Classify text data that has multiple independent labels. (mathworks.com)
Running the test program multiple times will simply add more data to the experiment. (lu.se)

Mapping short-read sequences against multiple alternative references. (lu.se)
Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. (lu.se)

Rapid sequencing will, in the near future, provide patients access to information that will help guide their day-to-day clinical care. (tgen.org)
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)

[ 12 ] and this "Cambridge Sequence" was subject to minor revisions in 1999. (medscape.com)

To find the global optimum for n sequences this way has been shown to be an NP-complete problem. (wikipedia.org)
When we read the cache, after the timeout, if we find the USN (sequence number) has actually changed, then the cache won't be valid. (samba.org)
I am then to find the amino acid that these DNA sequences encode per codon (each group of three literals. (unix.com)
Whether you're looking for Modular Sequence Valve, Pressure Sequence Valve, Inexplicable Performance Pressure Sequence Valve etc, you can explore and find the best products from Tradeindia. (tradeindia.com)
Third, unless your sequence is very short, you will always want to find sequences similar to yours, not just identical. (questel.com)

Convert decimal strings to Roman numerals using a recurrent sequence-to-sequence encoder-decoder model with attention. (mathworks.com)

In Oracle how do I save a sequence.nextval in a variable to be reused in multiple inserts? (stackexchange.com)
Inserts the next sequence number for the specified items. (microsoft.com)

Anatomy2

Organisms6

Chemicals and Drugs26

Analytical, Diagnostic and Therapeutic Techniques and Equipment29

Phenomena and Processes64

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science29

Health Care14

Genomes8

Next Generation Sequencing5

Nucleotide sequences1

Alignment of the sequences1

Acute myeloid2

Abstract1

Gene9

Proteins4

Reads2

Bulk1

Alignments8

Algorithms4

Visualization1

Phylogenetic2

Genes1

Adaptive2

Mutation2

Repertoire2

MRNA1

Genomic1

Nucleic1

Genetic3

Estimation1

Typically1

Protein sequence3

Biological4

Approaches7

Genbank1

Repeats2

Analysis5

Myeloma4

Annotation1

Consensus1

Isolates1

Predictors2

Describe2

Accession1

Variations2

Analyze1

Single3

Search1

Exon1

Last sequence1

Pairwise sequence1

Combine2

Differences1

Functions1

Copies2

Data5

Mapping2

Clinical2

19991

Find5

Roman1

Inserts2