Sequence assembly. Medical search. Frequent questions

This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. (wikipedia.org)
Expressed sequence tag or EST assembly was an early strategy, dating from the mid-1990s to the mid-2000s, to assemble individual genes rather than whole genomes. (wikipedia.org)
For instance, genomes often have large amounts of repetitive sequences, concentrated in the intergenic regions. (wikipedia.org)
In this 35-minute webinar, learn to perform NGS sequence assembly and alignment for multiple genomes, exomes, and RNA-Seq samples from a desktop or laptop computer. (dnastar.com)
However, sequence assemblies of most plant genomes remain fragmented. (cas.cz)
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)
Since many sequencing technologies produce reads that are significantly shorter than the target genome size, a process to construct contigs, scaffolds, and full-length genomes is needed. (biomedcentral.com)
The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. (biomedcentral.com)
Highly accurate long-read HiFi sequencing data for five complex genomes. (crossref.org)
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. (crossref.org)
We base this system on the physical isolation of viruses from large pooled samples of human serum and plasma ( e.g., discarded specimens from diagnostic laboratories), followed by shotgun sequencing of the resulting genomes. (cdc.gov)
Facilitated by the relative ease with which viruses can be isolated from seawater (using commercial filters), investigators in this area have examined a broad and essentially unbiased population of viral agents at the genome sequence level (including phage) and estimated the number of different genomes present (~5,000) ( 1 - 3 ). (cdc.gov)
These samples would be pooled and processed by using available technology to isolate virus particles en masse, recover viral nucleic acids, produce amplified shotgun libraries, carry out shotgun sequencing of the mixture of viral genomes, and reconstruct these genomes in silico with the techniques originally developed to sequence the entire human genome from random fragments. (cdc.gov)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)
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)
Sequencing the entire genome of an organism is a difficult problem, because all sequencing technologies to date have limitations on the length of the molecule that they can read (much smaller than the genomes of a vast majority of organisms). (irb.hr)
The main problem in both approaches stems from the repeating regions in the genomes which, if longer than the reads, prevent complete assembly of the genome. (irb.hr)
With the development of next generation sequencing (NGS) technologies, such as the Roche and Illumina platforms, new strategies are being used to characterize plant mitochondrial genomes. (springeropen.com)
This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes. (upf.edu)
While the transfer of already existing genes from one cell to another characterized an earlier phase of the field of biotechnology, synthetic biology involves the design, assembly, synthesis, or manufacture of new genomes, biological pathways, devices or organisms not found in nature. (cdc.gov)
Data for this research includes hundreds of re-sequenced genomes from three endangered species, complemented by chromosome-level assemblies, offering a robust foundation for comprehensive genomic analyses. (lu.se)

Specifically, the lawsuit focuses on Invitae's patent 10,604,799, or '799, which the company said is not "routine and conventional" and improves upon prior art by grouping DNA sequencing reads into contigs, aligning to a reference genome, and then realigning the original reads to the contigs. (genomeweb.com)
Sequencher will automatically compare the forward and the reverse-complement orientations to assemble the best possible contigs, so you can assemble DNA sequences regardless of orientation. (genecodes.com)
Despite the primary long-read assembly being ' quite excellent' , sex chromosome contigs were shorter than autosomal contigs, with repetitive sequences proving particularly problematic to resolve. (nanoporetech.com)
We have used gamma-ray induced 'early flowering mutant' to generate draft genome sequences with total length (bp) with 678,650,699 and contigs at 447,500 with N50 at 1,423 using the Illumina HiSeqX10 sequencing platform. (biorxiv.org)
Chromosome level genome assembly of Dendrobium huoshanense species was used to RagTag scaffold the available contigs of mutant, where it contained total length of 687,254,899 bp with N50 value 2,096. (biorxiv.org)
Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. (cas.cz)
In order to select reliable SNPs, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. (auburn.edu)
15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. (biomedcentral.com)
These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing. (biomedcentral.com)
Reference-mapping requires a closely-related genome as input to align reads, while de novo assembly generates contigs without the use of a reference genome. (biomedcentral.com)
Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. (biomedcentral.com)
This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. (biomedcentral.com)

On the other hand, some genes are expressed (transcribed) in very high numbers (e.g., housekeeping genes), which means that unlike whole-genome shotgun sequencing, the reads are not uniformly sampled across the genome. (wikipedia.org)

These data are used for a wide variety of important biological analyzes, including genome sequencing, comparative genomics, transcriptome analysis, and personalized medicine but are complicated by the volume and complexity of the data involved. (umd.edu)
Here, we report first de novo whole genome sequencing and assembly of an early flowering gamma mutant of Emma White hybrid for developing a genomics resource for further studies. (biorxiv.org)
Two different technologies were used for sequencing the mango genome, ~100x Illumina paired end coupled with 10X Genomics. (agri.gov.il)

Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. (tropmedres.ac)
PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality. (tropmedres.ac)
Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. (lu.se)

Nanopore sequencing offers advantages in all areas of research. (nanoporetech.com)
Brian has applied ultra-long nanopore sequencing reads to solve a piece of ' this real interesting biological puzzle' that is this vole's atypical sex chromosomes. (nanoporetech.com)
They therefore performed nanopore sequencing with ultra-long reads to bridge these contig gaps. (nanoporetech.com)
The need for technologies that would produce longer reads which could solve the problem of repeating regions has resulted in the advent of new sequencing approaches - the so-called third generation sequencing technologies which currently include two representatives: Pacific Biosciences (PacBio) and Oxford Nanopore. (irb.hr)
Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ. (upf.edu)

Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. (biomedcentral.com)
For many years, Sanger sequencing has been used to complement classical epidemiological and laboratory methods for investigating viral infections [ 1 ]. (biomedcentral.com)
Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. (frontiersin.org)
We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches. (lu.se)
We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches to reflect the heterogeneity across the data. (lu.se)
Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1. (cdc.gov)

Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript (ESTs). (wikipedia.org)
In order to determine the genetic blueprint of an organism, sequencing platforms typically employ the shotgun sequency strategy to oversample the target genome with a library of relatively short overlapping reads. (wncg.org)
The basic process (left vertical series of steps) depends on physical isolation and shotgun sequencing to obtain sequences of frequent. (cdc.gov)
2015 ), have been successfully assembled through a combination approach using shotgun and paired-end NGS sequencing from non-enriched whole genome DNA libraries. (springeropen.com)

There are three approaches to assembling sequencing data: De-novo: assembling sequencing reads to create full-length (sometimes novel) sequences, without using a template (see de novo sequence assemblers, de novo transcriptome assembly) Mapping/Aligning: assembling reads by aligning reads against a template (AKA reference). (wikipedia.org)
A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genomic sequencing projects. (aaai.org)
Our newly updated Cloud Assemblies workflow, which allows you to align virtually any size data set to a reference without the need to upgrade your computer hardware. (dnastar.com)
Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. (cas.cz)
Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. (tropmedres.ac)
Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. (frontiersin.org)
Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. (frontiersin.org)
Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations. (frontiersin.org)
providing sequencing data suitable to addressing challenging and outstanding problems in plant systematics. (frontiersin.org)
From the existing ASG methods, it is observed most of the researchers ignored/not-considered few of the assembly information such as assembly stability data and mechanical feasibility data due to higher complexity in retrieving it from CAD environment. (nitrkl.ac.in)
Assembly of the data by NRGene resulted in 571 super-scaffolds and ~80% coverage of the haploid mango genome (~490Mb). (agri.gov.il)
2010) Assembly algorithms for next-generation sequencing data. (omictools.com)
Based on 30 SARS-CoV-2 RT-PCR-positive specimens from inpa- available data, seven (2%) vaccine breakthrough cases§§ were tients and outpatients to CDPHE for sequencing each week. (cdc.gov)
Sović, Ivan (2016) Algorithms for de novo genome assembly from third generation sequencing data . (irb.hr)
Affordable commercial availability of the sequencing technology and algorithmic methods which can leverage the data could open doors to a vast number of very important applications, such as diagnosis and treatment of chronic diseases through personalized medicine or identification of pathogenic microorganisms from soil, water, food or tissue samples. (irb.hr)
Instead, the focus of the work conducted in the scope of this thesis is to develop novel methods for de novo DNA assembly from third generation sequencing data, which provide enough sensitivity and precision to completely omit the error-correction phase. (irb.hr)
We generated the mt genome sequence from 454 pyrosequencing whole genome big data. (springeropen.com)
Sarah Gregory] Ok, so what does sequence data in a public health lab do for us? (cdc.gov)
Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)
It allows us to quickly generate huge amounts of data and DNA sequence in a very short period of time. (cdc.gov)
Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (cdc.gov)
So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (cdc.gov)
I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (cdc.gov)
This hands on course will give you the experience and provide the tools that are needed to analyze next generation sequencing data. (lu.se)
Although the Entrez Genome Project database does not include viral genome sequencing projects, data from those projects are submitted to GenBank and are available in the Entrez Nucleotide and Entrez Genome databases. (lu.se)
After sequencing, data will be kept by CTG for 3 months and subsequently deleted . (lu.se)
Demultiplexed data files generated from the Illumina sequencing run. (lu.se)

Transcribed genes contain many fewer repeats, making assembly somewhat easier. (wikipedia.org)
To better understand these processes, we have assembled the entire 2.5-Mb mouse IgH (Igh) V region sequence of the C57BL/6 strain from public sequences and present the first complete annotated map of the region, including V genes, pseudogenes, repeats, and nonrepetitive intergenic sequences. (nih.gov)
We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. (cas.cz)
We are interested in how LRR proteins evolved, the self-assembly properties of individual repeats and the rational design of protein binders using this versatile scaffold. (lu.se)

Our RNA service includes mRNA and total RNA library preparation and sequencing on Illumina platforms. (lu.se)

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)
In order to obtain the sequence of an entire genome, reads need to be either stitched together (assembled) in a de novo fashion when the genome of the organism is unknown in advance, or mapped and aligned to the reference genome if one exists (reference assembly or mapping). (irb.hr)

Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. (wncg.org)

The genome completeness for Emma White RagTag scaffold assembly was assessed to be 93.6% complete using BUSCO v5.2.1 against the Viridiplantae odb10 orthologous dataset. (biorxiv.org)
The inter- and intra- specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding selection and whole genome association studies. (auburn.edu)
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)

it only takes a few mouse clicks to obtain the assembly of any gene family of interest, in contrast to other approaches that require some amount of scripting. (biomedcentral.com)

The aim of this study is to understand if the production of GABA in bifidobacteria is a strain-specific feature, analyzing the genomic sequence of 1,022 bifidobacterial strains belonging to the currently known 77 Bifidobacterium taxa, representing 70 species and seven subspecies, coupling the in silico information with an in vitro measurements of GABA levels generated by these bacteria. (nature.com)
We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. (springeropen.com)

This video provides an overview of the techniques and steps of preparing samples, DNA, and libraries for PacBio Single Molecule, Real-Time (SMRT) Sequencing to be used in de novo assembly projects. (pacb.com)
Phased diploid genome assembly with single-molecule real-time sequencing. (crossref.org)

that's a really solid contig for most peoples' assemblies , not their actual read generation' . (nanoporetech.com)
The GC content of genome was 33.48%, and predicted 95,529 genes from contig assembly. (biorxiv.org)
Over 300,000 putative SNPs have been identified, of which over 48,000 are high quality SNPs as defined by contig size of at least four sequences and the minor allele presence of at least twice in the contig. (auburn.edu)
To assess how well individual gene sequences are assembled , we report the percentage of sequence covered by the longest contig that maps to a given reference sequence. (biomedcentral.com)
To assess how well gene sequences are detected for different organisms, we report the number of organisms for which the longest mapped contig covers at least half of the corresponding reference sequence. (biomedcentral.com)

We have identified clusters of conserved region-specific intergenic sequences and have verified our assembly by genic and intergenic Southern blotting. (nih.gov)
This complete and definitive assembly of the mouse Igh V region will facilitate detailed study of promoter function and large-scale mechanisms associated with V(D)J recombination including locus contraction and antisense intergenic transcription. (nih.gov)
Methods: S. mutans samples were isolated from the saliva of 30 children with varying histories of dental caries, and they were characterized according to morphological and biochemical markers and the sequences of their 16S-23S intergenic spacer region. (bvsalud.org)
By sequencing the 16S-23S intergenic region, it was found that all of the isolates belonged to the species S. mutans . (bvsalud.org)
In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)

The designed algorithms pretends not to violate those rules because rules violation adversely affects the activity on the assembly line. (upv.es)
The two most common graph algorithms employed by de novo assembly programs are: overlap graphs for overlap-layout-consensus (OLC) methods, and k-mer based graphs for de Bruijn graph (DBG) methods. (biomedcentral.com)
2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. (omictools.com)
Both technologies are characterized, aside from long reads, by high error rates which existing assembly algorithms of the time were not capable of handling. (irb.hr)

Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. (tropmedres.ac)
Next, the isolates were differentiated by sequencing a specific region of the gene encoding the enzyme glucosyltransferase B ( gtfB ). (bvsalud.org)
Based on the genetic similarity of the isolates and pattern of amino acid variations identified by partial sequencing of the gtfB gene, base-pair changes were identified and correlated with different virulence patterns among the isolates. (bvsalud.org)

Two fundamental computations in computational biology are read alignment and genome assembly. (umd.edu)

In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. (wikipedia.org)
Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (cdc.gov)
Sarah Gregory] I understand that the ability of this sequencing to work optimally is dependent on bioinformatics. (cdc.gov)

Narzisi and Mishra, 2011) Comparing de novo genome assembly: the long and short of it. (omictools.com)

To investigate where these Y genes might be on the X chromosome, they performed amplicon sequencing of Y genes, and discovered that these genes amplified in both sexes. (nanoporetech.com)

Homen de Mello and Sanderson proposed the AND/OR graph notation to represent all feasible assembly sequences for a given assembly in one graph and also provide an algorithm to generate the AND/OR graph. (umanitoba.ca)
To perform optimal feasible assembly sequence generation efficiently, an effective computer aided automated method is developed and executed at two phases. (nitrkl.ac.in)

See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)

In our evaluation, we find that the MEGAN assembler performs best in terms of the percentage of reference genes covered and percentage of reference gene sequences detected. (biomedcentral.com)
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)

Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking. (auburn.edu)
Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. (frontiersin.org)
2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. (omictools.com)
Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. (upf.edu)
However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. (lu.se)
Our project seeks to unravel these mysteries by examining how genetic redundancy through duplicated sequences, like orthologs, and the role of non-coding elements such as transposable elements (TEs), contribute to species resilience during and after population bottlenecks. (lu.se)

OLC methods involve determining overlaps by performing a series of pair-wise sequence alignments. (biomedcentral.com)
The defining feature of the protein-alignment-guided assembly is that it uses existing protein alignments to detect DNA overlaps between reads. (biomedcentral.com)
Using the net alignments for the builds of the human and chimpanzee genome assemblies, we identified a total of 1,576 putative regions of inverted orientation , covering more than 154 mega-bases of DNA . (bvsalud.org)
Assembly of the alignments into full transcripts and quantification of the expression levels of each gene/transcript. (lu.se)

Revealing how molecular interactions are optimized to control both oligomerization state and assembly pathway in protein assemblies is of vital importance for our understanding of biomedically important biological assemblies, as well as for efforts to manipulate them. (lu.se)

Microbiome sequencing projects typically collect tens of millions of short reads per sample. (biomedcentral.com)
Large protein assemblies are typically held together by weak interactions between individual components but the multiplicity of interactions among the large number of subunits can lead to exquisite specificity. (lu.se)

DNA sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. (aaai.org)
Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. (biomedcentral.com)
These methods basically use assembly contact analysis, part transformations and laws of equilibrium & balancing of rigid bodies. (nitrkl.ac.in)
Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. (bvsalud.org)
CDC used whole genome sequencing (WGS) analysis to link one case to contaminated opened powdered formula from the patient's home and the other to contaminated breast pump equipment. (medscape.com)

The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. (cas.cz)
The final assembly was 20 pseudomolecules corresponding to the 20 chromosomes in the haploid genome. (agri.gov.il)

Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (biomedcentral.com)

In this video, a PacBio scientist covers how to assess DNA quantity and purity, size-selection of DNA libraries, and provides and introduction to SMRT Sequencing, including the benefits of long-reads when generating high-quality genome assemblies. (pacb.com)
In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. (biomedcentral.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)

Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (cdc.gov)

Here, we analyse sequence gaps in the current reference genome sequence of barley cv. (cas.cz)
have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. (tropmedres.ac)

1 Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations. (upenn.edu)
2 Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior. (upenn.edu)
Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way. (biomedcentral.com)
In this paper, we present a new approach to gene-centric assembly that we call protein-alignment-guided assembly . (biomedcentral.com)
The main technical contribution of this paper is the design and implementation of a "protein-alignment-guided" assembly algorithm that is explicitly designed for gene-centric assembly. (biomedcentral.com)
Distributed Many-to-Many Protein Sequence Alignment Using Sparse Matrices. (crossref.org)
Protein assembly continues until the ribosome encounters a "stop" codon (a sequence of three nucleotides that does not code for an amino acid). (medlineplus.gov)
These operations are made possible by recent advances in DNA synthesis and DNA sequencing, providing standardized DNA "parts," modular protein assemblies, and engineering models. (cdc.gov)
Protein assemblies are some of the most complex molecular machines in nature. (lu.se)
In a series of 3 papers, we analyzed the structure, developed structure prediction tools, and design tools, for different protein assemblies. (lu.se)
In another paper, we developed methods to predict large cubic symmetrical protein assemblies, such as viral capsids, from sequence. (lu.se)
The atomic interactions between subunits in protein assemblies are finely tuned to control affinity as well as quaternary structure. (lu.se)
We use computational protein design methods to change protein sequence in order to modify the oligomerization properties of coiled coils. (lu.se)
Our goal is to achieve molecular level control of protein self-assembly. (lu.se)
We use structure based modeling and computational protein design methods to optimize the protein sequence of proteins and peptides in order to control their assembly. (lu.se)

Beginning in 2008 when RNA-Seq was invented, EST sequencing was replaced by this far more efficient technology, described under de novo transcriptome assembly. (wikipedia.org)
This large scale EST sequencing project would allow the identification of majority of catfish transcriptome. (auburn.edu)

2019. Assembly of long, error-prone reads using repeat graphs. (crossref.org)
https://apps.who.int/iris/bitstream/handle/10665/258940/9789241513029- eng.pdf;jsessionid=C6A90E3DB1149B96B9CAB2669677DAC6?sequence=1 last accessed on 20 March 2019. (who.int)
Sixty-eighth session of the UN General Assembly, 10-11 July 2014, New York, United Nations, 2014 https://www.who.int/nmh/events/2014/a-res-68-300.pdf l ast accessed on 5 April 2019. (who.int)
https://www.who.int/ncds/governance/third-un-meeting/en/ last accessed on 5 April 2019. (who.int)

The first sequence assemblers began to appear in the late 1980s and early 1990s as variants of simpler sequence alignment programs to piece together vast quantities of fragments generated by automated sequencing instruments called DNA sequencers. (wikipedia.org)
Subsequent to these efforts, several other groups, mostly at the major genome sequencing centers, built large-scale assemblers, and an open source effort known as AMOS was launched to bring together all the innovations in genome assembly technology under the open source framework. (wikipedia.org)
In general, with assembly, you should try at least a few different assemblers. (biostars.org)
Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. (biomedcentral.com)

The car sequencing problem: Overview of state-of-the-art methods and industrial case-study of the ROADEF'2005 challenge problem. (upv.es)
The first phase of research is mainly focused on representing the assembly information in a streamlined manner by considering all possible states of assembly configurations for ease of computerization and developing efficient methods to extract the assembly information automatically from CAD environment though Computer Aided Automation (CAA). (nitrkl.ac.in)
At the same time, marine virologists have developed efficient methods for concentrating, amplifying, and sequencing complex viral mixtures obtained from the ocean. (cdc.gov)
This caused the development of time-consuming read error correction methods which were applied as a pre- processing step prior to assembly. (irb.hr)
The results show that Aracon reduces the overall assembly time by at least 3x and up to even an order of magnitude less compared to the state-of-the-art methods, while retaining comparable or better quality of assembly. (irb.hr)

2012) Next-generation sequencing and large genome assemblies. (omictools.com)
2011) Limitations of next-generation genome sequence assembly. (omictools.com)
Sarah Gregory] And following on that, what is Next Generation Sequencing? (cdc.gov)
Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections. (who.int)

The input sequences for EST assembly are fragments of the transcribed mRNA of a cell and represent only a subset of the whole genome. (wikipedia.org)
The mRNA interacts with a specialized complex called a ribosome, which "reads" the sequence of mRNA nucleotides. (medlineplus.gov)

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. (crossref.org)

and (IV) Racon - a rapid consensus module for correcting raw assemblies. (irb.hr)

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. (arxiv.org)

Utilizing all four nucleobases, sequence-defined click nucleic acids (CNAs) were synthesized using a simple and scalabale solution-phase approach. (rsc.org)

Our approach yields a highly continuous assembly of the first human Y chromosome of African origin. (upf.edu)

A total of 600,000 sequencing attempts were made, generating a total of 438,321 quality ESTs. (auburn.edu)
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)

Recent advances in DNA sequencing technology have dramatically increased the scale and scope of DNA sequencing. (umd.edu)

The main contributions of this thesis are the following: (1) An object-oriented version of the assembly sequence algorithm to generate AND/OR graph notation is given. (umanitoba.ca)

Good and Rhoades characterized these polymer sequences in vitro and through co-expression in cells, demonstrating that coacervation specificity is hard-coded in the polypeptide chain. (upenn.edu)
Monomer-sequence information in synthetic copolyimides can be recognised by tweezer-type molecules binding to adjacent triplet-sequences on the polymer chains. (reading.ac.uk)

With the Cloud Assemblies parallel processing capabilities, multiple-sample assembly, variant calling, and normalization generally complete even faster than on the most powerful desktop computers. (dnastar.com)
Lasergene 17.4.2 is a minor release that includes improvements to the Variant Table in MegAlign Pro and a bug fix addressing an issue with merging unaligned sequences. (dnastar.com)
In this paper, an approach based on a new variant of Particle Swarm Optimization Algorithm (PSO) called the multi-state of Particle Swarm Optimization (MSPSO) is used to solve the assembly sequence planning problem. (ump.edu.my)

The assembly was improved using two previously published genetic maps encompassing ~5,000 SNP markers and a recombination block map (NRGene) to allow correct ordering of scaffolds within a pseudomolecule and merging of unincorporated scaffolds into pseudomolecules. (agri.gov.il)
The project will explore the hypothesis that duplicated sequences offer genetic redundancy, potentially crucial for survival post-bottleneck, by providing backup gene copies for essential functions or evolving new ones. (lu.se)

Sequencher's intuitive controls allow you to set your sequence assembly parameters and adjust them within seconds, allowing you to assemble your DNA fragments quickly and accurately. (genecodes.com)
2. Properly installed throughout the seals, directional sealing assembly does not make a mistake on the sealing direction, difficult to assemble to guide the assembly tool assembly seals, disable the screwdriver it is possible to break into the hardtop, seal. (terrekosen-hydraulic.com)

Anatomy41

Organisms15

Chemicals and Drugs86

Analytical, Diagnostic and Therapeutic Techniques and Equipment38

Phenomena and Processes80

Disciplines and Occupations2

Technology, Industry, Agriculture2

Information Science11

Health Care1

Genomes22

Contigs12

Housekeeping genes1

Genomics3

Annotation4

Nanopore5

Sanger6

Shotgun4

Data27

Repeats4

Illumina1

Organism2

Emergence of next-generation1

Dataset3

Approaches1

Genomic sequence2

Single Molecule2

Contig5

Intergenic5

Algorithms4

Isolates3

Alignment and genome assembly1

Bioinformatics3

Novo genome assembly1

Amplicon1

Feasible assembly2

HiFi1

Gene sequences2

Species6

Alignments4

Biological1

Typically2

Analysis7

Chromosomes2

Loci1

Libraries3

High-throughput1

Reference genome sequence2

Protein15

Transcriptome2

20194

Assemblers4

Methods5

Next-generation4

MRNA2

Variants1

Consensus1

Aligning1

Nucleic acids1

Chromosome1

ESTs2

Technology1

Generate1

Polymer2

Variant3

Genetic2

Assemble2