Exact word matches in rice pseudomolecules

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 1047-1051 ◽  
Author(s):  
Shaolin Liu ◽  
Nicholas A Tinker ◽  
Diane E Mather
Keyword(s):  
High Frequency ◽  
Genomic Sequence ◽  
Oryza Sativa L ◽  
Rice Genome ◽  
Low Frequency ◽  
Nucleotide Position ◽  
Genome Wide ◽  
Transposon Activity ◽  
Simple Sequence ◽  
Oligonucleotide Sequence

Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones. Low-frequency zones contained occasional high-frequency spikes; these may represent footprints of RIM2 transposon activity. BLASTn searches of high-frequency non-SSR (simple sequence repeat) 18 bp oligos returned few sequences from species other than rice. These results demonstrate that, in rice, words are not randomly used between different regions within the same genome, and indicate that words that are frequently repeated within the rice genome tend to be unique to rice.Key words: oligonucleotide, sequence repetition, word match frequency, rice.

Frequency of microsatellite sequences in rice (Oryza sativa L.)

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1170-1176 ◽  
Author(s):  
Olivier Panaud ◽  
Xiuli Chen ◽  
Susan R. McCouch
Keyword(s):  
Genomic Library ◽  
Oryza Sativa L ◽  
Rice Genome ◽  
Cdna Libraries ◽  
Sequence Length ◽  
Tetranucleotide Repeat ◽  
Hybridization Probes ◽  
Microsatellite Map ◽  
Dissociation Temperature ◽  
Simple Sequence

This study was undertaken to estimate the relative frequencies of 13 microsatellite motifs in the rice genome as a basis for efficient development of a microsatellite map. Two dinucleotide, seven trinucleotide, and four tetranucleotide repeat motifs were end labelled and used as hybridization probes to screen genomic and cDNA libraries of rice, cv. IR36. Optimal washing temperatures for identification of clones containing specific microsatellite motifs were estimated based on washing temperatures near Td (dissociation temperature; Td = Tm − 7.6 °C). Sequencing of 20 putatively positive clones corresponding to each of 4 microsatellite motifs suggested that while Td provides a useful predictor of washing stringency for most of the repeats studied, those with a very high GC or AT content were most prone to error. The results from screening the rice genomic library suggest that there are an estimated 1360 poly(GA)n and 1230 poly(GT)n microsatellites in the rice genome, and that the relative frequency of different repeats decreased with increasing size of the motif. The most frequently observed microsatellites in the cDNA library were the same as for the genomic library, but no poly(CGG)n, poly(ATC)n, or tetranucleotide motifs were observed among cDNAs in this study.Key words: microsatellite, simple sequence repeat, SSR, simple sequence length polymorphism, SSLP.

Allelism and molecular mapping of soybean necrotic root mutants

Genome ◽  
2008 ◽  
Vol 51 (4) ◽  
pp. 243-250 ◽  
Author(s):  
Reid G. Palmer ◽  
Lei Zhang ◽  
Zhiping Huang ◽  
Min Xu
Keyword(s):  
High Frequency ◽  
Molecular Mapping ◽  
Mapping Population ◽  
Low Frequency ◽  
Flower Color ◽  
Somatic Tissue ◽  
Chemical Mutagenesis ◽  
Glycine Max L ◽  
Mutant Lines ◽  
Simple Sequence

Mutability of the w4 flower color locus in soybean, Glycine max (L.) Merr., is conditioned by an allele designated w4-m. Germinal revertants recovered among self-pollinated progeny of mutable plants have been associated with the generation of necrotic root mutations, chlorophyll-deficiency mutations, and sterility mutations. A total of 24 necrotic root mutant lines were generated from a total of 24 independent reversion events at the w4-m locus. The initial mutable population included 4 mutable categories for w4-m, designated (1) low frequency of early excisions, (2) low frequency of late excisions, (3) high frequency of early excisions, and (4) high frequency of late excisions. These mutable categories were based upon flower phenotype, i.e., somatic tissue. A total of 22 of 24 necrotic root mutations occurred from germinal reversions classified in the high frequency of excision categories. Of these 22 mutants, 14 came from early excisions and 8 came from late excisions. These necrotic root mutants were allelic to 6 previously identified necrotic root mutants derived from the study of germinal revertants, i.e., gene tagging studies, chemical mutagenesis, and “spontaneous” occurrences from genetic crosses. Thus, all 30 necrotic root mutants in soybean are allelic. An F2 mapping population from the cross of Minsoy (Rn1 Rn1) × T328 (rn1 rn1) was used to map the Rn1 locus using simple sequence repeat (SSR) markers. The Rn1 locus was located between Satt288 and Satt612 on molecular linkage group G.

scholarly journals Genome-Wide Identification of Sequence Variations and SSR Marker Development in the Munake Grape Cultivar

2021 ◽  
Vol 9 ◽  
Author(s):  
Haixia Zhong ◽  
Fuchun Zhang ◽  
Xiaoming Zhou ◽  
Mingqi Pan ◽  
Juan Xu ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Agronomic Traits ◽  
Entire Genome ◽  
Single Nucleotide ◽  
Grape Cultivar ◽  
Insertion And Deletion ◽  
Genome Wide ◽  
Sequence Variations ◽  
Polymerase Chain ◽  
Simple Sequence

The Munake grape cultivar produces uniquely flavored and high-quality fruits. Despite the numerous beneficial agronomic traits of Munake, there are few genetic resources available for this cultivar. To address this knowledge gap, the entire genome was sequenced using whole-genome sequencing approaches and compared with a Vitis vinifera L. reference genome. This study describes more than 3 million single nucleotide polymorphism (SNP), 300,000 insertion and deletion (InDel), 14,000 structural variation (SV), and 80,000 simple sequence repeat (SSR) markers (one SSR per 4.23 kb), as well as their primers. Among the SSRs, 44 SSR primer pairs were randomly selected and validated by polymerase chain reaction (PCR), allowing discrimination between the different Munake cultivar genotypes. The genetic data provided allow a deeper understanding of Munake cultivar genomic sequence and contribute to better knowledge of the genetic basis behind its key agronomic traits.

scholarly journals Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

2020 ◽  
Author(s):  
Hanna Amoanimaa-Dede ◽  
Jiacheng Zhang ◽  
Chuntao Su ◽  
Hongbo Zhu
Keyword(s):  
Ssr Markers ◽  
Ipomoea Batatas ◽  
Genomic Sequence ◽  
Average Frequency ◽  
Genetic Studies ◽  
Germplasm Identification ◽  
Cultivar Development ◽  
Genome Wide ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Background: Sweetpotato is a multifunctional root crop with many essential nutrients and bioactive compounds. Due to its genetic complexity and lack of genomic resources, efficient genetic studies, and cultivar development lags far behind other major crops. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweetpotato. Results: To further explore new SSR markers and accelerate its use in sweetpotato genetic studies, genome-wide characterization and development of SSR markers were performed using the recently published genome of sweetpotato cultivar, Taizhong6. In this study, a set of 2,431 primer pairs were developed from 133,727 SSRs identified in the sweetpotato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. 50% of the 100 randomly selected primer pairs amplified 251 alleles and the average number of alleles was 5.02 alleles per locus with a range of 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweetpotato materials into four clusters at a similarity coefficient of 0.68. Conclusion: The SSR markers currently developed will provide valuable genetic resources for germplasm identification, genetic diversity analysis, and functional genomics studies in sweetpotato and related species.

Simulations of high-resolution images of amorphous silicon films

1986 ◽  
Vol 44 ◽  
pp. 544-545
Author(s):  
G. Y. Fan ◽  
J. M. Cowley
Keyword(s):  
Electron Microscope ◽  
High Frequency ◽  
Fourier Transformation ◽  
Amorphous Materials ◽  
Low Frequency ◽  
Chromatic Aberration ◽  
Structure Information ◽  
Frequency Components ◽  
High Resolution Images ◽  
Spatial Frequency Spectrum

It is well known that the structure information on the specimen is not always faithfully transferred through the electron microscope. Firstly, the spatial frequency spectrum is modulated by the transfer function (TF) at the focal plane. Secondly, the spectrum suffers high frequency cut-off by the aperture (or effectively damping terms such as chromatic aberration). While these do not have essential effect on imaging crystal periodicity as long as the low order Bragg spots are inside the aperture, although the contrast may be reversed, they may change the appearance of images of amorphous materials completely. Because the spectrum of amorphous materials is continuous, modulation of it emphasizes some components while weakening others. Especially the cut-off of high frequency components, which contribute to amorphous image just as strongly as low frequency components can have a fundamental effect. This can be illustrated through computer simulation. Imaging of a whitenoise object with an electron microscope without TF limitation gives Fig. 1a, which is obtained by Fourier transformation of a constant amplitude combined with random phases generated by computer.

SEM image sharpness analysis

1996 ◽  
Vol 54 ◽  
pp. 142-143
Author(s):  
M. T. Postek ◽  
A. E. Vladar
Keyword(s):  
High Frequency ◽  
Low Frequency ◽  
Quantitative Information ◽  
Primary Electron ◽  
Image Sharpness ◽  
Critical Dimensions ◽  
Sem Image ◽  
Frequency Changes ◽  
Electron Microscopes ◽  
Scanning Electron

Fully automated or semi-automated scanning electron microscopes (SEM) are now commonly used in semiconductor production and other forms of manufacturing. The industry requires that an automated instrument must be routinely capable of 5 nm resolution (or better) at 1.0 kV accelerating voltage for the measurement of nominal 0.25-0.35 micrometer semiconductor critical dimensions. Testing and proving that the instrument is performing at this level on a day-by-day basis is an industry need and concern which has been the object of a study at NIST and the fundamentals and results are discussed in this paper.In scanning electron microscopy, two of the most important instrument parameters are the size and shape of the primary electron beam and any image taken in a scanning electron microscope is the result of the sample and electron probe interaction. The low frequency changes in the video signal, collected from the sample, contains information about the larger features and the high frequency changes carry information of finer details. The sharper the image, the larger the number of high frequency components making up that image. Fast Fourier Transform (FFT) analysis of an SEM image can be employed to provide qualitiative and ultimately quantitative information regarding the SEM image quality.

Real Ear Sound Pressure Levels Developed by Three Portable Stereo System Earphones

1992 ◽  
Vol 1 (4) ◽  
pp. 52-55 ◽  
Author(s):  
Gail L. MacLean ◽  
Andrew Stuart ◽  
Robert Stenstrom
Keyword(s):  
High Frequency ◽  
Sound Pressure ◽  
Low Frequency ◽  
Test System ◽  
Output Frequency ◽  
Frequency Effects ◽  
Adult Men ◽  
Frequency Responses ◽  
Significant Difference ◽  
Sound Pressure Levels

Differences in real ear sound pressure levels (SPLs) with three portable stereo system (PSS) earphones (supraaural [Sony Model MDR-44], semiaural [Sony Model MDR-A15L], and insert [Sony Model MDR-E225]) were investigated. Twelve adult men served as subjects. Frequency response, high frequency average (HFA) output, peak output, peak output frequency, and overall RMS output for each PSS earphone were obtained with a probe tube microphone system (Fonix 6500 Hearing Aid Test System). Results indicated a significant difference in mean RMS outputs with nonsignificant differences in mean HFA outputs, peak outputs, and peak output frequencies among PSS earphones. Differences in mean overall RMS outputs were attributed to differences in low-frequency effects that were observed among the frequency responses of the three PSS earphones. It is suggested that one cannot assume equivalent real ear SPLs, with equivalent inputs, among different styles of PSS earphones.

Evaluation of Special Hearing Aids for Deaf Children

1971 ◽  
Vol 36 (4) ◽  
pp. 527-537 ◽  
Author(s):  
Norman P. Erber
Keyword(s):  
Hearing Aids ◽  
High Frequency ◽  
Hearing Aid ◽  
Low Frequency ◽  
Acoustic Stimulation ◽  
Deaf Children ◽  
Frequency Range ◽  
Frequency Limit ◽  
Unpublished Studies ◽  
Published Research

Two types of special hearing aid have been developed recently to improve the reception of speech by profoundly deaf children. In a different way, each special system provides greater low-frequency acoustic stimulation to deaf ears than does a conventional hearing aid. One of the devices extends the low-frequency limit of amplification; the other shifts high-frequency energy to a lower frequency range. In general, previous evaluations of these special hearing aids have obtained inconsistent or inconclusive results. This paper reviews most of the published research on the use of special hearing aids by deaf children, summarizes several unpublished studies, and suggests a set of guidelines for future evaluations of special and conventional amplification systems.

Efeitos do Método Pilates sobre a variabilidade da frequência cardíaca, flexibilidade e variáveis antropométricas em indivíduos sedentários

2016 ◽  
Vol 17 (1) ◽  
pp. 66
Author(s):  
Maria Lina Silva Leite
Keyword(s):  
High Frequency ◽  
Low Frequency

O objetivo deste estudo foi avaliar os efeitos do Método Pilates sobre a variabilidade da frequência cardíaca, na flexibilidade e nas variáveis antropométricas em indivíduos sedentários. O presente estudo contou com 14 voluntárias do sexo feminino, na faixa etária entre 40 e 55 anos, que realizaram 20 sessões de exercícios do Método Pilates, duas vezes por semana, com duração de 45 minutos cada sessão, dividida em três fases: repouso, exercício e recuperação. As variáveis estudadas foram: os dados antropométricos, flexibilidade avaliada utilizando o teste de sentar-e-alcançar com o Banco de Wells, e intervalos R-R usando um cardiotacômetro. O processamento dos sinais da frequência cardíaca foi efetuado em ambiente MatLab 6.1®, utilizando a TWC. Os dados coletados foram submetidos ao teste de normalidade de Shapiro Wilk e foi utilizado o teste de Wilcoxon e Anova One Way (α = 0,05). Nos resultados, observou-se que não houve diferenças significativas entre os valores antropométricos e de frequência cardíaca, porém houve aumento da flexibilidade com o treinamento. Comparando a primeira e a vigésima sessão com relação aos parâmetros low frequency (LF), high frequency (HF), e relação LF/HF, não houve diferença na fase de repouso e foram constatadas diferenças significativas de LF (p = 0,04) e HF (p = 0,04) na fase de exercício e diferença significativa de LF/HF (p = 0,05) na fase de recuperação. Comparando os parâmetros nos períodos de repouso, exercícios e recuperação durante a primeira sessão e durante a vigésima sessão, não houve diferença significativa nos parâmetros LF, HF e LF/HF. Pode-se concluir que, em relação à flexibilidade, foi observada uma melhora significativa, enquanto a análise da frequência cardíaca caracterizou a intensidade do exercício de 50% da capacidade funcional das voluntárias. Em relação aos parâmetros LF, HF e LF/HF foram observados um aumento da variabilidade da frequência cardíaca, provavelmente produto da atividade do Método Pilates. A Transformada Wavelet (TWC) mostrou-se um Método adequado para as análises da variabilidade da frequência cardíaca.Palavras-chave: frequência cardíaca, Transformada Wavelet, Pilates.

Dynamics of the processes in metal machining

1998 ◽  
Vol 2 ◽  
pp. 115-122
Author(s):  
Donatas Švitra ◽  
Jolanta Janutėnienė
Keyword(s):  
High Frequency ◽  
Machine Tools ◽  
Metal Cutting ◽  
Cutting Tool ◽  
Low Frequency ◽  
Metal Cutting Machine ◽  
Cutting Machine ◽  
Metal Machining

In the practice of processing of metals by cutting it is necessary to overcome the vibration of the cutting tool, the processed detail and units of the machine tool. These vibrations in many cases are an obstacle to increase the productivity and quality of treatment of details on metal-cutting machine tools. Vibration at cutting of metals is a very diverse phenomenon due to both it’s nature and the form of oscillatory motion. The most general classification of vibrations at cutting is a division them into forced vibration and autovibrations. The most difficult to remove and poorly investigated are the autovibrations, i.e. vibrations arising at the absence of external periodic forces. The autovibrations, stipulated by the process of cutting on metalcutting machine are of two types: the low-frequency autovibrations and high-frequency autovibrations. When the low-frequency autovibration there appear, the cutting process ought to be terminated and the cause of the vibrations eliminated. Otherwise, there is a danger of a break of both machine and tool. In the case of high-frequency vibration the machine operates apparently quiently, but the processed surface feature small-sized roughness. The frequency of autovibrations can reach 5000 Hz and more.

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