scholarly journals SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9372
Author(s):  
Wei Luo ◽  
Qing Wu ◽  
Lan Yang ◽  
Pengyu Chen ◽  
Siqi Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Selective Breeding ◽  
Low Frequency ◽  
Polymorphic Markers ◽  
Comparative Transcriptome ◽  
Multiple Sequence ◽  
Polymorphic Ssrs ◽  
Polymorphic Microsatellites ◽  
Almost All ◽  
Validation Experiments

Microsatellite (SSR) markers are the most popular markers for genetic analyses and molecular selective breeding in plants and animals. However, the currently available methods to develop SSRs are relatively time-consuming and expensive. One of the most factors is low frequency of polymorphic SSRs. In this study, we developed a software, SSREnricher, which composes of six core analysis procedures, including SSR mining, sequence clustering, sequence modification, enrichment containing polymorphic SSR sequences, false-positive removal and results output and multiple sequence alignment. After running of transcriptome sequences on this software, a mass of polymorphic SSRs can be identified. The validation experiments showed almost all markers (>90%) that were identified by the SSREnricher as putative polymorphic markers were indeed polymorphic. The frequency of polymorphic SSRs identified by SSREnricher was significantly higher (P < 0.05) than that of traditional and HTS approaches. The software package is publicly accessible on GitHub (https://github.com/byemaxx/SSREnricher).

A novel method for large-scale identification of polymorphic microsatellites through comparative transcriptome analysis

2017 ◽  
Author(s):  
Wei Luo ◽  
Hongyue Qu ◽  
Xin Wang ◽  
Qin Zhan ◽  
Qiang Lin
Keyword(s):  
Transcriptome Analysis ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Genetic Research ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Polymorphic Ssrs ◽  
Validation Experiment ◽  
Almost All ◽  
The Cost

ABSTRACTMicrosatellite (SSR) is one of the most popular markers for applied genetic research, but generally the current methods to develop SSRs are relatively time-consuming and expensive. Although high-throughput sequencing (HTS) approach has become a practical and relatively inexpensive option so far, only a small percentage of SSR markers turn out to be polymorphic. Here, we designed a new method to enrich polymorphic SSRs through the comparative transcriptome analysis. This program contains five main steps: 1) transcriptome data downloading or RNA-seq; 2) sequence assembly; 3) SSR mining and enrichment of sequences containing SSRs; 4) sequence alignment; 5) enrichment of sequences containing polymorphic SSRs. A validation experiment was performed and the results showed almost all markers (> 90%) that were indicated as putatively polymorphic by this method were indeed polymorphic. The frequency of polymorphic SSRs was significantly higher (P < 0.05) but the cost and running time were much lower than those of traditional and HTS approaches. The method has a practical value for polymorphic SSRs development and might be widely used for genetic analyses in any species.

scholarly journals Post-Alignment Adjustment and Its Automation

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1809
Author(s):  
Xuhua Xia
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Position Weight Matrix ◽  
Pairwise Alignment ◽  
Amino Acid Sequences ◽  
Weight Matrix ◽  
Multiple Sequence ◽  
Manual Adjustment ◽  
Alignment Errors ◽  
Almost All

Multiple sequence alignment (MSA) is the basis for almost all sequence comparison and molecular phylogenetic inferences. Large-scale genomic analyses are typically associated with automated progressive MSA without subsequent manual adjustment, which itself is often error-prone because of the lack of a consistent and explicit criterion. Here, I outlined several commonly encountered alignment errors that cannot be avoided by progressive MSA for nucleotide, amino acid, and codon sequences. Methods that could be automated to fix such alignment errors were then presented. I emphasized the utility of position weight matrix as a new tool for MSA refinement and illustrated its usage by refining the MSA of nucleotide and amino acid sequences. The main advantages of the position weight matrix approach include (1) its use of information from all sequences, in contrast to other commonly used methods based on pairwise alignment scores and inconsistency measures, and (2) its speedy computation, making it suitable for a large number of long viral genomic sequences.

scholarly journals Experiment Investigation of Bistable Vibration Energy Harvesting with Random Wave Environment

2021 ◽  
Vol 11 (9) ◽  
pp. 3868
Author(s):  
Qiong Wu ◽  
Hairui Zhang ◽  
Jie Lian ◽  
Wei Zhao ◽  
Shijie Zhou ◽  
...  
Keyword(s):  
Renewable Energy ◽  
Energy Harvesting ◽  
Cantilever Beam ◽  
Large Scale ◽  
Low Frequency ◽  
Vibration Energy ◽  
Random Wave ◽  
Periodic Signal ◽  
Vibration Energy Harvesting ◽  
Motion Activity

The energy harvested from the renewable energy has been attracting a great potential as a source of electricity for many years; however, several challenges still exist limiting output performance, such as the package and low frequency of the wave. Here, this paper proposed a bistable vibration system for harvesting low-frequency renewable energy, the bistable vibration model consisting of an inverted cantilever beam with a mass block at the tip in a random wave environment and also develop a vibration energy harvesting system with a piezoelectric element attached to the surface of a cantilever beam. The experiment was carried out by simulating the random wave environment using the experimental equipment. The experiment result showed a mass block’s response vibration was indeed changed from a single stable vibration to a bistable oscillation when a random wave signal and a periodic signal were co-excited. It was shown that stochastic resonance phenomena can be activated reliably using the proposed bistable motion system, and, correspondingly, large-scale bistable responses can be generated to realize effective amplitude enlargement after input signals are received. Furthermore, as an important design factor, the influence of periodic excitation signals on the large-scale bistable motion activity was carefully discussed, and a solid foundation was laid for further practical energy harvesting applications.

scholarly journals A Novel Methodology for Adaptive Coordination of Multiple Controllers in Electrical Grids

Mathematics ◽  
2021 ◽  
Vol 9 (13) ◽  
pp. 1474
Author(s):  
Ruben Tapia-Olvera ◽  
Francisco Beltran-Carbajal ◽  
Antonio Valderrabano-Gonzalez ◽  
Omar Aguilar-Mejia
Keyword(s):  
Power Systems ◽  
Power System ◽  
Electric Power ◽  
Large Scale ◽  
Short Circuit ◽  
Dynamic Performance ◽  
Low Frequency ◽  
Electric Power System ◽  
Design Stage ◽  
Positive Interaction

This proposal is aimed to overcome the problem that arises when diverse regulation devices and controlling strategies are involved in electric power systems regulation design. When new devices are included in electric power system after the topology and regulation goals were defined, a new design stage is generally needed to obtain the desired outputs. Moreover, if the initial design is based on a linearized model around an equilibrium point, the new conditions might degrade the whole performance of the system. Our proposal demonstrates that the power system performance can be guaranteed with one design stage when an adequate adaptive scheme is updating some critic controllers’ gains. For large-scale power systems, this feature is illustrated with the use of time domain simulations, showing the dynamic behavior of the significant variables. The transient response is enhanced in terms of maximum overshoot and settling time. This is demonstrated using the deviation between the behavior of some important variables with StatCom, but without or with PSS. A B-Spline neural networks algorithm is used to define the best controllers’ gains to efficiently attenuate low frequency oscillations when a short circuit event is presented. This strategy avoids the parameters and power system model dependency; only a dataset of typical variable measurements is required to achieve the expected behavior. The inclusion of PSS and StatCom with positive interaction, enhances the dynamic performance of the system while illustrating the ability of the strategy in adding different controllers in only one design stage.

scholarly journals Optimizing the Frequency Capping: A Robust and Reliable Methodology to Define the Number of Ads to Maximize ROAS

2021 ◽  
Vol 11 (15) ◽  
pp. 6688
Author(s):  
Jesús Romero Leguina ◽  
Ángel Cuevas Rumin ◽  
Rubén Cuevas Rumin
Keyword(s):  
High Frequency ◽  
Large Scale ◽  
Low Frequency ◽  
Digital Marketing ◽  
Optimal Frequency ◽  
Novel Technique ◽  
Maximum Threshold

The goal of digital marketing is to connect advertisers with users that are interested in their products. This means serving ads to users, and it could lead to a user receiving hundreds of impressions of the same ad. Consequently, advertisers can define a maximum threshold to the number of impressions a user can receive, referred to as Frequency Cap. However, low frequency caps mean many users are not engaging with the advertiser. By contrast, with high frequency caps, users may receive many ads leading to annoyance and wasting budget. We build a robust and reliable methodology to define the number of ads that should be delivered to different users to maximize the ROAS and reduce the possibility that users get annoyed with the ads’ brand. The methodology uses a novel technique to find the optimal frequency capping based on the number of non-clicked impressions rather than the traditional number of received impressions. This methodology is validated using simulations and large-scale datasets obtained from real ad campaigns data. To sum up, our work proves that it is feasible to address the frequency capping optimization as a business problem, and we provide a framework that can be used to configure efficient frequency capping values.

Separatrix crossing and large scale diffusion in low-frequency three-wave systems

1998 ◽  
Vol 58 (3) ◽  
pp. 3768-3776 ◽  
Author(s):  
B. Weyssow ◽  
J. D. Reuss ◽  
J. Misguich
Keyword(s):  
Large Scale ◽  
Low Frequency ◽  
Separatrix Crossing
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