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Second generation sequencing
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Next-generation sequencing has allowed for the identification of different genetic variations, which are known to contribute to diseases. Of these, insertions and deletions are the second most abundant type of variations in the genome, but their biological importance or disease association is not well-studied, especially for deletions of intermediate sizes.
15p
vibransone
28-03-2024
3
2
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Ebook "Disease gene identification: Methods and protocols (Second edition)" presents detailed laboratory procedures in an easy to follow format that can be carried out with success by investigators lacking previous exposure to a specific research method. Chapter guide readers through the application of molecular approaches to disease gene identification and overviews, and case studies are also presented.
396p
lucchinguyen
28-12-2023
5
2
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Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking.
16p
vigalileogalilei
27-02-2022
9
1
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The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally.
20p
vigalileogalilei
27-02-2022
14
1
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Third-generation sequencing technologies have advanced the progress of the biological research by generating reads that are substantially longer than second-generation sequencing technologies. However, their notorious high error rate impedes straightforward data analysis and limits their application. A handful of error correction methods for these error-prone long reads have been developed to date.
17p
vigalileogalilei
27-02-2022
9
1
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Dorystaechas hastata is a relict endemic medicinal and aromatic plant under risk of extinction. Assessment of genetic diversity and association between geographic distribution and genetic variation could benefit to the conservation efforts. The objectives of this study were to assess genetic diversity and population differentiation of the species in its natural habitat.
18p
tudichquannguyet
29-11-2021
11
1
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In the present study, the transcriptome profiles of A. pumila leaf tissues treated with 250 mM NaCl for 0, 0.5, 3, 6, 12, 24 and 48 h were analyzed using a combination of second-generation sequencing (SGS) and third-generation single-molecule real-time (SMRT) sequencing.
14p
vitzuyu2711
29-09-2021
12
1
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Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than second-generation sequencing technologies such as Illumina. The increased read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and characterize the intra-species variations.
14p
visilicon2711
20-08-2021
14
1
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Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads.
15p
viansan2711
30-07-2021
17
1
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Dunaliella salina is a good model organism for studying salt stress. In order to have a global understanding of the expression profiles of Dunaliella salina in response to hypersaline stress, we performed quantitative transcriptomic analysis of Dunaliella salina under hypersaline stress (2.5 M NaCl) of different time duration by the second and third generation sequencing method.
17p
vijeeni2711
24-07-2021
13
0
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Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads.
12p
vikentucky2711
26-11-2020
16
1
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Analyzing next-generation sequencing data is difficult because datasets are large, second generation sequencing platforms have high error rates, and because each position in the target genome (exome, transcriptome, etc.) is sequenced multiple times.
10p
vioklahoma2711
19-11-2020
9
1
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The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs can be achieved using microarray or second generation sequencing (SGS) data.
5p
viflorida2711
30-10-2020
8
2
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PacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes.
9p
viconnecticut2711
28-10-2020
19
2
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Cancer as a worldwide problem is driven by genomic alterations. With the advent of high-throughput sequencing technology, a huge amount of genomic data generates at every second which offer many valuable cancer information and meanwhile throw a big challenge to those investigators.
17p
vijisoo2711
27-10-2020
12
0
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Third-generation sequencing platforms, such as PacBio sequencing, have been developed rapidly in recent years. PacBio sequencing generates much longer reads than the second-generation sequencing (or the next generation sequencing, NGS) technologies and it has unique sequencing error patterns. An effective read simulator is essential to evaluate and promote the development of new bioinformatics tools for PacBio sequencing data analysis.
7p
vijisoo2711
27-10-2020
28
1
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: Fragmentation at random nucleotide locations is an essential process for preparation of DNA libraries to be used on massively parallel short-read DNA sequencing platforms. Although instruments for physical shearing, such as the Covaris S2 focused-ultrasonicator system.
13p
viuchiha2711
21-04-2020
6
0
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In the present paper, we introduce a new sequence of linear positive operators with the help of generating functions. We obtain some Korovkin type approximation properties for these operators and compute rates of convergence by means of the first and second order modulus of continuities and Peetre’s K-functional.
13p
danhdanh27
07-01-2019
26
1
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The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called “next-generation” sequencing.
16p
danhdanh11
11-01-2019
13
2
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In this paper we present a modification of the second-order step-size algorithm. This modification is based on the so called "forcing functions". It is proved that this modified algorithm is well-defined. It is also proved that every point of accumulation of the sequence generated by this algorithm is a second-order point of the nonlinear programming problem.
7p
vinguyentuongdanh
20-12-2018
19
0
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