Representation base sequence. Medical search. Frequent questions

De novo identification tools such as LTRharvest determine the position of potential LTR retrotransposon or ERV insertions in genomic sequences. (uni-hamburg.de)
However, understanding of quantitative traits and use of genomic tools for breeding is partly restricted by the large expected genome size of 3,947 to 4,397 Mbp/1C ( Arumuganathan and Earle, 1991 ) and the occurrence of highly repetitive sequences in the pea genome. (frontiersin.org)
For the new study, members of the team from Washington University's Genome Institute tackled the lamprey genome with whole-genome shotgun sequencing, fosmid sequencing, and BAC library sequencing, using genomic DNA from a female sea lamprey caught wild in the Great Lakes. (genomeweb.com)
Collaborators at the MSU Genomic Core sequenced lamprey RNA, meanwhile, generated transcriptome data that helped in annotating the newly sequenced genome. (genomeweb.com)
Residual amounts of amplified genomic DNA are minimized and do not interfere with mitochondrial-specific downstream methods such as qPCR or direct Sanger sequencing. (qiagen.com)
Following crRNA and tracrRNA hybridization, SpCas9 is targeted to genomic loci matching a 20-nt guide sequence within the crRNA, immediately upstream of a required 5′-NGG protospacer adjacent motif (PAM) 11 . (cdc.gov)

Bidirectional Encoder Representations from Transformers BERT (Devlin et al. (kdnuggets.com)
Of course, GPT-3 and GPTs may grab headlines, but it belongs to a much larger superfamily of transformer models, including a plethora of variants based on the Bidirectional Encoder Representations from Transformers (BERT) family originally created by Google, as well as other smaller families of models from Facebook and Microsoft. (kdnuggets.com)

Several reduced-representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. (wur.nl)
In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. (rochester.edu)
based on amplification methods that use primers and We present an alternative approach for rapid, sensitive, probes designed to detect specific organisms. (cdc.gov)
The base tious organisms still relies largely on culture methods and compositions of strategically selected regions of the microscopy, which were as important in the recent identi- genome are used to identify and distinguish organisms in fication of the severe acute respiratory syndrome-associat- the sample. (cdc.gov)
Broad-range polymerase chain reaction (PCR) methods increased affinity and base pairing selectivity (18,19). (cdc.gov)
WGP TM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. (frontiersin.org)
Although traditional methods only capture the linear correlations of ICS features, our deep industrial representation learning model (DIRL) based on a convolutional neural network can mine high-order features, thus solving the problem of high-dimensional and heterogeneous ICS data. (techscience.com)
Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
In this blog post, we discuss some of the fundamental advantages of our Pan-Genome approach compared to other linear or graph-based methods. (sevenbridges.com)
Due to its high processivity and strand displacement activity, REPLI-g DNA Polymerase is capable of amplifying up to 100 kb without dissociating from the DNA template and minimizes unequal sequence and locus representation compared with PCR-based amplification methods. (qiagen.com)
The aim of this project is to explore quantum computing based methods for solving lattice protein problems. (lu.se)
METHODS: Based on the Beijing Functional Community Cohort, 4392 participants who underwent three health examinations (2015, 2016, and 2017) were followed up for incident T2D until the end of 2021. (bvsalud.org)
Traditionally, the gold standard for DST is culture-based phenotypic methods. (msdmanuals.com)

Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. (nature.com)
Several of the isolates used in this study sequence alignments of all available CoV nucleotide did not have a genome sequence record in GenBank. (cdc.gov)
The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. (frontiersin.org)
This sequence-based physical map will be useful to assemble the genome sequence of pea. (frontiersin.org)
WGP is designed based on the use of sequence tags generated by next generation sequencing (NGS) and is a powerful alternative to traditional DNA fingerprinting based physical mapping technologies, and also simultaneously generates a partial genome sequence. (frontiersin.org)
Genome sequence-based curation of PubMLST data challenges interspecies recombination in the Burkholderia cepacia complex. (cdc.gov)
Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data. (cdc.gov)

Reduced representation bisulfite sequencing (RRBS) is an efficient and high-throughput technique for analyzing the genome-wide methylation profiles on a single nucleotide level. (wikipedia.org)
Due to the high cost and depth of sequencing to analyze methylation status in the entire genome, Meissner et al. (wikipedia.org)

Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. (frontiersin.org)
While homologous to conserved non-coding sequences in the jawed vertebrate genomes, though, the lamprey versions of these elements shared sequence identity over around half of each element, on average. (genomeweb.com)
and in sequencing of entire genomes of viruses from numerous different strains. (who.int)

Figure 2: N50 contig sizes from assemblies generated from sequence data for each sequencing platform. (nature.com)
Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, sequence quality data and nucleotide alignments with translations. (metacpan.org)
The length of the meta data sequence is not dependent on the amount of the meta information. (metacpan.org)
Character based meta data is read and set by method meta() and its variants. (metacpan.org)
Edit: Dylan, in answer to your question below, the incorporation of varying fixed point data (as in the base space here) is just the kind of thing Bredon cohomology is designed for. (mathoverflow.net)
It accepts sequence data in a variety of formats and a basic LTR annotation in GFF3format as input. (uni-hamburg.de)
The method has also been reported to perform well on problems similar to the classification of sequence data, such as the classification of text documents, that have a high-dimensional feature space and sparse data ( 16 ). (asm.org)
Three challenges in this field are learning effective representation from high-dimensional features, data heterogeneity, and data noise due to the diversity of data dimensions, formats and noise of sensors, controllers and actuators. (techscience.com)
The success of machine learning algorithms largely depends on feature selection and data representation [ 5 , 6 ]. (techscience.com)
Because these approaches will rely on novel data types such as DNA sequences and high-throughput phenotyping images, Breeding 4 will call for analyses that are complementary to traditional quantitative genetic studies, being based on machine learning techniques which make efficient use of sequence and image data. (springer.com)
In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)
corralm, a CA-based method for multi-table batch integration of scRNAseq data in shared latent space. (ne.jp)
DMAP components can filter and process aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. (otago.ac.nz)
The test data download unpacks into a directory named test_MDS_data containing fastq sequence reads and sam files from bismark mapping. (otago.ac.nz)
1: Chatterjee A, Stockwell P A, Rodger E J, and Morison I M, Comparison of alignment software for genome-wide bisulphite sequence data , Nucleic Acids Research Volume 40, Issue 10Pp. (otago.ac.nz)
Seven Bridges GRAF™ Suite comprises bioinformatics workflows and tools for secondary analysis of next generation sequencing (NGS) data, based on a pan-genome graph reference. (sevenbridges.com)
GRAF™ Pan Genome Reference - contains both small variants (SNPs and INDELs up to several dozens of base-pairs in length) as well as larger structural variants, which are typically difficult to identify from short-read sequencing data. (sevenbridges.com)
Traditionally, epidemiology has been based on data collected by public health agencies through health personnel in hospitals, doctors' offices, and out in the field. (plos.org)
Web-based data mining is having a revolutionary impact on the way we monitor global health outcomes and behaviors. (plos.org)
Bytes - A simple refcounted data type representing an immutable sequence of zero or more bytes from an unspecified origin. (valadoc.org)
Sequence - The Sequence struct is an opaque data type representing a sequence data type. (valadoc.org)
SequenceIter - The SequenceIter struct is an opaque data type representing an iterator pointing into a Sequence . (valadoc.org)
Partitioning environmental sequencing data. (myexperiment.org)
What Should Health Departments Do with HIV Sequence Data? (cdc.gov)
Users have the possibility to share data they own (or have share credentials for) to other users of the same BASE installation. (lu.se)
BASE features a biomaterial LIMS tracking biological material from its source to hybridisation/sequencing and ultimately to raw data and analysis. (lu.se)
One of the important features of BASE is its capabilities as a local data repository. (lu.se)
A BASE project is used to group items (biomaterial, raw data, and experiments) into a logical entity, and a BASE experiment is a collection of bioassays, e.g., array data, grouped logically together for further analysis. (lu.se)
Data privacy is guarded by the data owner and BASE allows the owner to set data access rules. (lu.se)
To this end, each item in BASE is owned by a user enabling him to share data with colleagues. (lu.se)
BASE has an integrated file system to provide the possibility for researchers to collect all data files related to a project in one single storage location. (lu.se)
The file storage is an integral part of a strategy to store all experiment relevant data in BASE, even data types not already supported in analysis. (lu.se)
BASE features a hierarchically organised analysis interface that allows data filtering, normalisation, transformation, and other analyses. (lu.se)
By exploiting the inherently estimates even when only a few data snapshots are available, low displacement rank, together with the development of suitable although the improved performance comes at a cost of a Gohberg-Semencul (GS) representations, and the use of data de- pendent trigonometric polynomials, the proposed time-recursive considerable computational complexity. (lu.se)
represent a data sequence interest in finding alternative time-varying spectral estimation under consideration, whereof subsets of length L may be techniques. (lu.se)
Define the data and robustness to model assumptions, there has been a particular frequency vectors interest in data-dependent filterbank-based algorithms. (lu.se)

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)
We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins. (rochester.edu)
Sequence-specific dynamic information in proteins. (rochester.edu)
Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. (rochester.edu)
A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. (medscimonit.com)
Simplified lattice-based models provide a means for exploring the basics of the sequence-structure relationship of proteins. (lu.se)

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)
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)

The workflow accepts input reads in FASTQ, CRAM or BAM format, produces graph-based alignments in BAM or CRAM format, and outputs variant calls in VCF format. (sevenbridges.com)
Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. (cdc.gov)

When RRBS was first developed, Sanger sequencing was initially used. (wikipedia.org)

Three benchtop high-throughput sequencing instruments are now available. (nature.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)
Further complicating the sequencing process is the genome's preponderance of guanine and cytosine bases, which can befuddle some high-throughput sequencing instruments, leading to an over- or under-representation of these GC reads. (genomeweb.com)

Global informatics and physical property selection in protein sequences. (rochester.edu)
Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. (rochester.edu)
Beyond supersecondary structure: the global properties of protein sequences. (rochester.edu)

Through comparisons with sequences from jawed animals, researchers saw shared chromosomal organization between the lamprey and these gnathostomes. (genomeweb.com)
As a consequence, experimental optical DNA maps are typically not complete representations of the chromosomal DNA sequence. (lu.se)

Non-Invasive Prenatal Testing is often performed by utilizing read coverage-based profiles obtained from shallow whole genome sequencing to detect fetal copy number variations. (tudelft.nl)
Here, we identified the coding sequence of the EZH2 gene and characterized its expression pattern in fetal tissues of Duroc pigs at 65- and 90-day postcoitus (dpc). (hindawi.com)
In this study, we identified a transcript variant of EZH2 in porcine fetal tissues by cloning and sequencing. (hindawi.com)

It combines restriction enzymes and bisulfite sequencing to enrich for areas of the genome with a high CpG content. (wikipedia.org)
The fragments that comprise the reduced genome still include the majority of promoters, as well as regions such as repeated sequences that are difficult to profile using conventional bisulfite sequencing approaches. (wikipedia.org)
DNA fragments of 40-220 base pair are representative of the majority of promoter sequences and CpG islands Bisulfite conversion: The DNA fragments are then bisulfite converted, which is a process that deaminates unmethylated cytosine into a uracil. (wikipedia.org)
PCR amplification: The bisulfite converted DNA is then amplified using PCR with primers that are complementary to the sequence adapters. (wikipedia.org)

This strategy has been successfully from large groupings of organisms, electrospray ionization used with consensus 16S ribosomal RNA primers for deter- mass spectrometry for accurate mass measurements of PCR products, and base composition signature analysis to mining bacterial diversity, both in environmental samples identify organisms in a sample. (cdc.gov)
The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). (asm.org)
Today, rRNA-based analysis remains a central method in microbiology, used not only to explore microbial diversity but also as a day-to-day method for bacterial identification. (asm.org)
In 2002, an ad hoc committee for the reevaluation of species definition in bacteriology ( 24 ) advised that all new bacterial species descriptions include an rRNA sequence from the type strain, and in 2001, Bergey's Trust published a revised higher-order taxonomy attempting to reconcile bacterial taxonomy with rRNA-based phylogeny ( 12 , 13 ). (asm.org)

For Illumina sequencing, 36-base single-end sequencing reads are most commonly performed. (wikipedia.org)
The 454 GS Junior generated the longest reads (up to 600 bases) and most contiguous assemblies but had the lowest throughput (70 Mb/run, 9 Mb/h). (nature.com)
Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. (frontiersin.org)

Sequence alignment and analysis: Due to the unique properties of RRBS, special software is needed for alignment and analysis. (wikipedia.org)
Alignment to a reference genome allows the programs to identify base pairs within the genome that are methylated. (wikipedia.org)
Beyond Supersecondary Structure: Physics-Based Sequence Alignment. (rochester.edu)
It is able to identify protein coding regions associated with the retrotransposition process as well as internal regulatory features using local alignment and hidden Markov model-based algorithms. (uni-hamburg.de)

Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without a reference genome. (wur.nl)
are applicable to biobanks associated with genome, and the development of genomics population-based studies coordinated by databases and new bioinformatics tools. (who.int)

Starting in the mid-1980s, Carl Woese revolutionized the field of microbiology with his rRNA-based phylogenetic comparisons delineating the three main branches of life ( 28 ). (asm.org)
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)

This class defines an abstract interface for basic residue-based meta information. (metacpan.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)
Almost 35 percent of the existing genome assembly is made up of sequences representing repetitive elements from thousands of families, researchers reported. (genomeweb.com)
Although becoming less commonly used, the array production LIMS of previous BASE versions is retained to support researchers with spotting facilities, e.g., protein array production and BAC array printing that may not be commercially available. (lu.se)

Sequence adapters: Methylated sequence adapters are ligated to the DNA fragments. (wikipedia.org)
Sequencing: The fragments are then sequenced. (wikipedia.org)
WGP technology is based on generation of short sequence tags from terminal ends of restriction fragments of individual BAC clones, followed by assembly of BAC clones into contigs based on shared regions containing identical sequence tags. (frontiersin.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)

begingroup$ The Serre spectral sequence is functorial. (mathoverflow.net)
It is true that each element of the group gives a map of spectral sequences. (mathoverflow.net)
If you construct the Serre spectral sequence in the usual way, there is a non-equivariantly inconsequential choice of base point in the base space. (mathoverflow.net)
You do not get to collate your actions one element of the group at a time into an algebraically meaningful action of the group on "the" spectral sequence. (mathoverflow.net)
Then there is an equivariant Serre spectral sequence, developed by Moerdijk and Svensson: The equivariant Serre spectral sequence. (mathoverflow.net)
Numerical simulations together with theoretical of the various IAA-based batch spectral estimation techniques complexity measures illustrate the achieved performance gain. (lu.se)

To address the challenges of accurate assembly of the pea genome (∼4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. (frontiersin.org)
In the current study, we have undertaken construction of a sequence-based physical map of pea to address the challenge in the assembly of these repetitive sequences and overcome the shortcomings of traditional restriction digestion based physical maps. (frontiersin.org)
Despite its potential for providing insights into vertebrate evolution, though, the lamprey genome had previously proven tough to sequence, authors of the current study explained, owing to the its extensive repetitive element content and the lack of a related reference sequence. (genomeweb.com)
Even so, they explained that repeats may actually make up a somewhat larger proportion of the overall lamprey genome, since some repetitive element sequences are unwittingly collapsed by genome assembly software. (genomeweb.com)

Molecule's representation in 3D. (pte.hu)
3. Molecule's building based on their Lewis-formula and/or sequence. (pte.hu)
Such maps serve as a coarse-grained representation - fingerprint - of a DNA molecule's sequence. (lu.se)

To understand how weather and meteorological sequence variables affect crop yield, the positional encoding used in Transformers is typically shared across different sample sequences. (ijcai.org)
Such screening typically operates on a discretized binned representation of the genome, where (ab)normality of bins of a set size is judged relative. (tudelft.nl)

Now, next generation sequencing approaches are used. (wikipedia.org)
We have developed a series of novel approaches to protein biophysics based on ideas from information theory and sign. (rochester.edu)
Beside GAPDA and SPRDA, with recent in-depth advances on graph theory and network science, various biomedical entity association prediction (EAP) approaches based on graph convolutional network (GCN) [ 14 ] have been proposed. (biomedcentral.com)

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

The drawback of this approach could identify and distinguish between SARS and other for epidemiologic applications is that the analysis of PCR known CoV, including the human CoV 229E and OC43, products for mixed amplified samples requires sequencing individually and in a mixture of all 3 human viruses. (cdc.gov)
Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed. (google.com)
Using this foundation, BERT breaks the familiar left-to-right indoctrination that is inherent in earlier text analysis and representation models. (kdnuggets.com)
The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. (asm.org)
formed a Fourier analysis based on the random walk represen- erties in terms of thermodynamical and kinetic behavior, tation. (lu.se)
wavelength corresponding to -helix structure, as one might have statistical analysis on the sequences that fold well indicates expected, but also at large wavelengths. (lu.se)
permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)
Afterward, iPiDi-PUL extracted key features and conducted dimension reduction by principal component analysis over feature vector based on positive unlabeled learning [ 11 ]. (biomedcentral.com)
The selection of analysis tools depends on array type and available plug-ins where a wide range of tools are pre-installed with BASE, and optional plug-ins can be downloaded from the BASE plug-in site . (lu.se)
The sequence y(n) of "almost non-cyclic" vectors follows the formula y(n+1) = y(n) + r(T) y(n), which will allow for efficient use of elementary Fourier Analysis. (lu.se)

Although this is technically an application of algebraic geometry and representation theory to TCS, they were led to introduce new quantum groups and new purely algebro-geometric and representation-theoretic ideas in their pursuit of P vs NP. (stackexchange.com)

In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. (asm.org)
There were 9 amino acid insertions and an amino acid substitution in this transcript compared with the validated reference sequence in NCBI. (hindawi.com)

Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest. (frontiersin.org)

Accurate whole human genome sequencing using reversible terminator chemistry. (nature.com)
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)
We find that CAREER forms accurate predictions of job sequences, achieving state-of-the-art predictive performance on three widely-used economics datasets. (nips.cc)
We propose a novel transformer based architecture for accurate and robust crop yield prediction, by introducing a Customized Positional Encoding (CPE) that encodes a sequence adaptively according to static information associated with the sequence. (ijcai.org)
To develop and evaluate a web-based tool for rapid and accurate genotyping of noroviruses and Polymerase sapoviruses. (cdc.gov)
The web-based HuCaT tool supports rapid and accurate genotyping of human noroviruses and sapoviruses. (cdc.gov)

Similarity Studies of Corona Viruses through Chaos Game Representation. (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)

If the range is not defined, it defaults to the complete sequence. (metacpan.org)
More research is needed to know just why that is, the group explained, though it may reflect either rapid sequence change in the lamprey lineage or else a splitting off by the lamprey ancestor prior to complete sequence conservation in the jawed vertebrates. (genomeweb.com)

Transformers are the most visible and impactful application of attention in machine learning and, while transformers have mostly been used in NLP, the biological inspiration for attention is loosely based on the vision systems of animals. (kdnuggets.com)

The following is an example of how an input sequence is represented in BERT. (kdnuggets.com)

Building on theories from case-based learning and adaptive learning, the goal of this research is to develop the case adaptation mechanism for adaptive case-based learning in web-based environment by designing the adaptive case-based learning model and using both artificial neural network and case-based reasoning techniques so that the proposed mechanism is capable of reasoning and planning multilayer pedagogic knowledge. (ncl.edu.tw)
Computers, however, have no facility in this regard, and LLMs (large language models) based on neural nets, such as ChatGPT, are a case in point. (evolutionnews.org)
This technology based on the sequence-to-sequence architecture for neural machine translation defines how to efficiently train a multilingual system extendable to new languages and modalities while allowing knowledge transfer. (upc.edu)

The method is based on multiple displacement amplification (MDA) technology, which carries out isothermal genome amplification utilizing a uniquely processive DNA polymerase. (qiagen.com)
In this paper, we describe the development and evaluation of an forces that drive norovirus evolution [ 9 , 10 ] and most frequently occur alternative web-based tool, Human Calicivirus Typing (HuCaT) tool for at the junction of the RdRp (polymerase) and VP1 (capsid) encoding typing of human norovirus and sapovirus sequences. (cdc.gov)
Many of the active NICs in the Region have optimal capacity for viral isolation, polymerase chain reaction, serological testing and sequencing. (who.int)

Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)
Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. (asm.org)

We prior knowledge of nucleic acid sequence information is use broad-range PCR to generate amplification products required to develop these tests, they are not able to identi- from the broadest possible grouping of organisms, followed fy unanticipated, newly emergent, or previously unknown by electrospray ionization mass spectrometry and base infectious organisms. (cdc.gov)

A DNA molecule forms a double-helix where the complementary interactions between bases strike a balance between stability (protecting the integrity of the double helix) and accessibility (for instance, the bases need to be accessible when reading the DNA sequence). (lu.se)

This has led to the development of graph-based references, able to naturally represent all polymorphisms, including insertions, deletions, and structural variation. (sevenbridges.com)

The results of this research provide the pedagogic assistance and reference, so as to support exact practical knowledge content in the adaptive case-based learning model, as well as make learners keep their learning motives with generating the further adapted learning content automatically. (ncl.edu.tw)
Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L. (frontiersin.org)
Material reflectance properties are then estimated for video sequences of a moving person captured under uniform ambient illumination by matching the observed local image statistics to the reference observations. (jvrb.org)
The representation of the human reference genome as a linear haploid DNA sequence poses limitations when trying to incorporate the known genetic diversity of human populations. (sevenbridges.com)

The results presented on standard test sequences illustrate the potential use of this system for object-based coding and representation of multimedia. (dcu.ie)

Alternative approach to protein structure prediction based on sequential similarity of physical properties. (rochester.edu)
ChatGPT seems to find some similarity between the sequence I put forward and the number pi. (evolutionnews.org)

Earthquake sequences induced by fluid disposal into the subsurface show strong variability in their magnitude distributions and clustering behavior. (copernicus.org)
Observations of earthquake sequences in Oklahoma and Kansas include some sequences that have near-Poissonian distribution of interevent times and robust foreshock sequences, while other sequences display more typical mainshock-aftershock clustering behavior. (copernicus.org)

The estimated reflectance properties are then transferred to image sequence observations of a dynamic scene by matching the observations in the static scene. (jvrb.org)
We attempt to untangle the processes that control the occurrence and evolution of disposal-induced earthquake sequences by integrating detailed seismicity observations, pore pressure modeling, and 3D physics-based earthquake simulations. (copernicus.org)

The bottom track contains a representation of a hierarchical LTR retrotransposon annotation graph, as reported by LTRdigest, collapsed into a single track. (uni-hamburg.de)
Here, we proposed an end-to-end model, referred to as PDA-PRGCN (PDA prediction using subgraph Projection and Residual scaling-based feature augmentation through Graph Convolutional Network). (biomedcentral.com)
Specifically, starting with the known piRNA-disease associations represented as a graph, we applied subgraph projection to construct piRNA-piRNA and disease-disease subgraphs for the first time, followed by a residual scaling-based feature augmentation algorithm for node initial representation. (biomedcentral.com)
GAPDA treated each known piRNA-disease association pair as a node in their reconstructed graph and employed graph attention network to make representation learning [ 12 ]. (biomedcentral.com)

A Transformer's architecture is purely based on self-attention, abandoning the RNN and CNN architectures commonly used for sequence modelling. (kdnuggets.com)

The WHO-endorsed GeneXpert MTB/RIF (Cepheid) is an automated closed system that uses rapid PCR techniques to detect DNA sequences in sputum samples that are specific for M. tuberculosis, as well as certain mutations that confer resistance to RIF. (msdmanuals.com)

Comparison of these results with another method based on information entropy revealed high accordance. (medscimonit.com)

RESULTS: High values of the rho-coefficient extracted sequences of strong structural determinability and structures of high sequence selectivity. (medscimonit.com)

To this end we develop CAREER, a transformer-based model that uses transfer learning to learn representations of job sequences. (nips.cc)

The team's analyses of the 816 million base genome assembly uncovered 26,046 predicted protein-coding genes. (genomeweb.com)
To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses. (cdc.gov)
We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)

2018) is a language representation model that combines the power of pre-training with the bi-directionality of the Transformer's encoder (Vaswani et al. (kdnuggets.com)

At this point a residue in a sequence object can have only one meta value. (metacpan.org)

The still image segmentation component is comprised of a conventional spatial segmentation algorithm (Recursive Shortest Spanning Tree (RSST)), a hierarchical segmentation representation method (Binary Partition Tree (BPT)), and user interaction. (dcu.ie)

Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. (cdc.gov)
The sequence of base pairs of DNA molecules is the genetic blueprint of any living being. (lu.se)

With MLM, instead of predicting the complete incoming sequence by going from left to right or vice versa, the model masks a percentage of tokens at random, and only predicts those masked tokens. (kdnuggets.com)
CONCLUSIONS: The results revealed sequence-to-structure (and vice versa) correlation in early-stage folding. (medscimonit.com)

This sequence appears to follow a pattern based on the positional value of digits (zero-based) in the decimal representation of pi (π). (evolutionnews.org)
We argue that it is necessary and beneficial to differentiate the positional encoding for distinct samples based on time-invariant properties of the sequences. (ijcai.org)

Anatomy28

Organisms9

Diseases2

Chemicals and Drugs34

Analytical, Diagnostic and Therapeutic Techniques and Equipment38

Psychiatry and Psychology59

Phenomena and Processes67

Disciplines and Occupations6

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Humanities3

Information Science36

Health Care10

Genomic6

Bidirectional Encoder Representations2

Methods13

Genome sequence7

Methylation2

Genomes3

Data37

Proteins6

Nucleotide2

Alignments2

Sanger1

High-throughput3

Protein sequences3

Chromosomal2

Fetal3

Bisulfite4

Bacterial4

Reads3

Alignment4

Bioinformatics2

Phylogenetic2

Abstract1

Researchers3

Fragments3

Matching principle1

Spectral6

Repetitive4

Molecule's3

Typically2

Approaches3

Traditionally1

Analysis10

Quantum1

NCBI2

Assignment1

Accurate6

Viruses2

Complete sequence2

Biological1

BERT1

Neural3

Polymerase3

Gene2

Generate1

Complementary1

Insertions1

Reference4

Illustrate1

Similarity2

Behavior2

Observations2

Graph4

Commonly1

Detect1

Entropy1

Selectivity1

Transformer-based1

Analyses3

Combines1

Residue1

Hierarchical1

Genetic2

Vice versa2

Positional2