scholarly journals ReferenceSeeker: rapid determination of appropriate reference genomes

2019 ◽  
Author(s):  
O. Schwengers ◽  
T. Hain ◽  
T. Chakraborty ◽  
A. Goesmann
Keyword(s):  
Rapid Determination ◽  
Single Nucleotide ◽  
Microbial Genomes ◽  
Polymorphism Detection ◽  
Command Line Tool ◽  
Subsequent Calculation ◽  
In Silico Analyses ◽  
Reference Genomes ◽  
Selection Of

AbstractSummaryThe large and growing number of microbial genomes available in public databases makes the optimal selection of reference genomes necessary for many in-silico analyses, e.g. single nucleotide polymorphism detection, scaffolding and comparative genomics, increasingly difficult. Here, we present ReferenceSeeker, a novel command line tool combining a fast kmer profile-based database lookup of candidate reference genomes with subsequent calculation of highly specific average nucleotide identity (ANI) values for the rapid determination of appropriate reference genomes. Pre-built databases for bacteria, archaea, fungi, protozoa and viruses based on the RefSeq database are provided for download.Availability and ImplementationReferenceSeeker is open source software implemented in Python. Source code and binaries are freely available for download at https://github.com/oschwengers/referenceseeker under the GNU GPL3 [email protected]

Rapid determination of trisomy 21 from amniotic fluid cells using single-nucleotide polymorphic loci

2005 ◽  
Vol 25 (12) ◽  
pp. 1138-1141 ◽  
Author(s):  
Bálint Nagy ◽  
Zoltán Bán ◽  
Levente Lázár ◽  
Richárd Gyula Nagy ◽  
Csaba Papp ◽  
...  
Keyword(s):  
Amniotic Fluid ◽  
Trisomy 21 ◽  
Rapid Determination ◽  
Single Nucleotide Polymorphic ◽  
Single Nucleotide ◽  
Polymorphic Loci ◽  
Amniotic Fluid Cells

Near-Infrared Spectroscopic Measurement of Organic Matter in Soil

2012 ◽  
Vol 499 ◽  
pp. 414-418
Author(s):  
Tao Pan ◽  
Zhen Tao Wu ◽  
Jie Mei Chen
Keyword(s):  
Organic Matter ◽  
Near Infrared ◽  
Rapid Determination ◽  
Nir Spectroscopy ◽  
Partial Least Square ◽  
Least Square ◽  
Modeling Prediction ◽  
Validation Set ◽  
Selection Of

Near-infrared (NIR) spectroscopy was successfully applied to chemical free and rapid determination of the organic matter in soil, and moving window partial least square (MWPLS) combining with Savitzky-Golay (SG) smoothing was used to the selection of NIR waveband. Thirty-five samples were randomly selected from all 97 collected soil samples as the validation set. The remaining 62 samples were divided into similar modeling calibration set (37 samples) and modeling prediction set (25 samples) based on partial least square cross-validation predictive bias (PLSPB). The selected waveband was 1896 nm to 2138 nm; the SG smoothing parameters and PLS factor OD, DP, NSP and F were 2, 6, 71 and 15, respectively; the modeling effect M-SEP and M-RPwere 0.219% and 0.944, respectively; the validating effect V-SEP and V-RPwere 0.243% and 0.878, respectively. The result provided a reliable NIR model and valuable references for designing specialized NIR instruments.

scholarly journals ReferenceSeeker: rapid determination of appropriate reference genomes

2020 ◽  
Vol 5 (46) ◽  
pp. 1994
Author(s):  
Oliver Schwengers ◽  
Torsten Hain ◽  
Trinad Chakraborty ◽  
Alexander Goesmann
Keyword(s):  
Rapid Determination ◽  
Reference Genomes

scholarly journals DNA Dizileme Temelli Haplotip Analizlerinde Kullanılan Bazı Yazılımlar

2019 ◽  
Vol 7 (sp1) ◽  
pp. 107
Author(s):  
Emel Tüten Sevim ◽  
Kemal Karabağ
Keyword(s):  
Sequence Analysis ◽  
Haplotype Analysis ◽  
Initial Step ◽  
Molecular Methods ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Genetic Potential ◽  
Pcr Technology ◽  
Selection Of

Determination of genetic resources and their diversity constitutes are the initial step of the breeding programs. Before starting to the selection of the desired properties, many molecular methods are used to determine the existing genetic potential and determine the genotypic values. Many molecular methods (RAPD, RFLP, AFLP, SSR and DNA sequencing etc.) based on PCR technology are used to identify populations, identify genes related to yield and resistance, and demonstrate phylogenetic relationships. Many software’s for the analysis of molecular datasets obtained from molecular methods have been developed and the field of bioinformatics was born. In this study, after DNA sequence analysis; it is aimed to give information about haplotype analysis by determining SNPs (Single Nucleotide Polymorphism's) in individuals of populations, calculation of the genetic distance among populations and within populations, and software and analysis used for phylogenetic tree drawing.

Weak Beam Imaging and Diffraction Studies of Stacking Faults in Silicon

1976 ◽  
Vol 34 ◽  
pp. 590-591
Author(s):  
T. Y. Tan ◽  
W. K. Tice
Keyword(s):  
Fast Neutron ◽  
Rapid Determination ◽  
Stacking Faults ◽  
Imaging Method ◽  
Large Reduction ◽  
Dislocation Loops ◽  
Fringe Spacing ◽  
Weak Beam ◽  
Kinematical Theory

In studying ion implanted semiconductors and fast neutron irradiated metals, the need for characterizing small dislocation loops having diameters of a few hundred angstrom units usually arises. The weak beam imaging method is a powerful technique for analyzing these loops. Because of the large reduction in stacking fault (SF) fringe spacing at large sg, this method allows for a rapid determination of whether the loop is faulted, and, hence, whether it is a perfect or a Frank partial loop. This method was first used by Bicknell to image small faulted loops in boron implanted silicon. He explained the fringe spacing by kinematical theory, i.e., ≃l/(Sg) in the fault fringe in depth oscillation. The fault image contrast formation mechanism is, however, really more complicated.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide

Methods for rapid determination of pecan (Carya illinoensis) seed viability

2017 ◽  
Vol 45 (2) ◽  
pp. 455-464
Author(s):  
T.T. Xue ◽  
J. Liu ◽  
Y.B. Shen ◽  
G.Q. Liu
Keyword(s):  
Rapid Determination ◽  
Seed Viability ◽  
Carya Illinoensis
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