Understanding Y haplotype matching probability

The accumulation course angle error of inertial navigation system will decrease the accuracy and reliability of an geomagnetism aided inertial navigation system using a geomagnetic contour matching algorithm. To improve the matching accuracy, the matching track and true track should be as parallel as possible. An improved geomagnetic matching algorithm is presented by introducing rotation angle search technique. To reduce the computation burden, improve operation efficiency and reduce false matching probability, a new search area determination method is proposed, which redefines the search region and reduces the search range. Simulation results demonstrate the effectiveness of the proposed algorithm and the improvement in the matching accuracy.

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Y-Haplotype X in the Balkans

International Journal of Anthropology ◽

10.1007/s11599-006-9017-y ◽

2006 ◽

Vol 21 (2) ◽

pp. 111-116

Author(s):

G. Mercier ◽

F. Diéterlen ◽

G. Lucotte

Keyword(s):

The Balkans ◽

Y Haplotype

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Y haplotype variability in a population of SÃO Paulo state, Brazil

Forensic Science International Genetics ◽

10.1016/j.fsigen.2016.05.003 ◽

2016 ◽

Vol 23 ◽

pp. e22-e23 ◽

Cited By ~ 2

Author(s):

M.M.S.G. Cardena ◽

A.J. Mansur ◽

A.C. Pereira ◽

C. Fridman

Keyword(s):

Sao Paulo ◽

São Paulo ◽

Paulo State ◽

São Paulo State ◽

Y Haplotype

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Relaxation Labeling for Contour Point Matching under Affine Transformations

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.380-384.3449 ◽

2013 ◽

Vol 380-384 ◽

pp. 3449-3452

Author(s):

Wei Wang ◽

Yong Mei Jiang ◽

Bo Li Xiong ◽

Gang Yao Kuang

Keyword(s):

Affine Transformations ◽

Point Matching ◽

Matching Criterion ◽

Relaxation Labeling ◽

Contour Point ◽

Soft Matching ◽

Matching Probability

A matching between two sets of points under affine transformations has attracted more and more attention. Many algorithms devote to extracting the descriptor for the point from the configuration, and the descriptor based point matching is achieved ignoring the pairwise geometric relations. In this paper, taking advantage of the inlier correspondences in matched configurations, we formalize a soft matching criterion which emerges from a matching probability matrix, followed by a relaxation labeling process to refine the match. The proposed approach has been implemented and gives encouraging results under rotation, scaling, shearing and noise.

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Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

Frontiers in Plant Science ◽

10.3389/fpls.2021.625416 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nataliya V. Melnikova ◽

Elena N. Pushkova ◽

Ekaterina M. Dvorianinova ◽

Artemy D. Beniaminov ◽

Roman O. Novakovskiy ◽

...

Keyword(s):

Genome Assembly ◽

Single Copy ◽

Dioecious Species ◽

Male And Female ◽

Male Genome ◽

Oxford Nanopore ◽

Genome Assemblies ◽

First Time ◽

High Quality Genome ◽

Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

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Could Rapidly Mutating Y-STRs be a Potential Forensic Tool in Discriminating Lebanese Monozygotic Twins?

Genetics & Applications ◽

10.31383/ga.vol2iss2pp35-42 ◽

2018 ◽

Vol 2 (2) ◽

pp. 35

Author(s):

Paula Romanos ◽

Jamilah Borjac

Keyword(s):

Twin Pair ◽

Monozygotic Twins ◽

Dna Profile ◽

Identifiler Plus ◽

Lineage Markers ◽

Dna Profiles ◽

Short Tandem Repeat Markers ◽

Genetic Analyzer ◽

Y Haplotype ◽

Short Tandem

Despite the high power of discrimination that characterizes the well identified 16 to 24 autosomal short tandem repeat markers, monozygotic twins differentiation is generally limited. Arising from a single fertilized egg, monozygotic twins share the same genotype therefore the same DNA profile. This situation imposes a challenge in forensics especially considering that lineage markers are in general less informative than autosomal ones. Although in some cases Y haplotype is considered a powerful investigative tool, it cannot distinguish males belonging to the same paternal lineage. The use of rapidly mutating Y-STRs with mutation rate above 1x10-2 that were recently included in forensic casework is presumed helpful. Since science is always dynamic and each population has its own characteristics, we aim in this study to distinguish between Lebanese monozygotic male twins using rapidly mutating Y-STRs. For this purpose, fourteen unrelated pairs of male monozygotic twins were recruited. Participants filled in a well-designed questionnaire and signed an informed consent. DNA was extracted using PureLink Genomic DNA Mini kit, genotyped using the Identifiler Plus kit, and separated on 3500 Genetic Analyzer to confirm the monozygosity status. DNA samples underwent a second amplification using the Y Filer Plus kit. According to our results, all the Y Filer Plus DNA profiles showed complete match for each twin pair. By consequence, the use of rapidly mutating Y-STRs in this study did not improve discrimination.

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Using Semantic Distance to Support Geometric Harmonisation of Cadastral and Topographical Data

ISPRS Annals of Photogrammetry Remote Sensing and Spatial Information Sciences ◽

10.5194/isprsannals-ii-2-15-2014 ◽

2014 ◽

Vol II-2 ◽

pp. 15-22 ◽

Cited By ~ 1

Author(s):

M.J. Schulze ◽

F. Thiemann ◽

M. Sester

Keyword(s):

Semantic Distance ◽

Correct Choice ◽

Machine Learning Techniques ◽

Major Influence ◽

Combine Data ◽

Learning Techniques ◽

Least Squares Adjustment ◽

Data Infrastructures ◽

Different Sources ◽

Matching Probability

In the context of geo-data infrastructures users may want to combine data from different sources and expect consistent data. If both datasets are maintained separately, different capturing methods and intervals leads to inconsistencies in geometry and semantic, even if the same reality has been modelled. Our project aims to automatically harmonize such datasets and to allow an efficient actualisation of the semantics. The application domain in our project is cadastral and topographic datasets. To resolve geometric conflicts between topographic and cadastral data a local nearest neighbour method was used to identify perpendicular distances between a node in the topographic and an edge in the cadastral dataset. The perpendicular distances are reduced iteratively in a constraint least squares adjustment (LSA) process moving the coordinates from node and edge towards each other. The adjustment result has to be checked for conflicts caused by the movement of the coordinates in the LSA. <br><br> The correct choice of matching partners has a major influence on the result of the LSA. If wrong matching partners are linked a wrong adaptation is derived. Therefore we present an improved matching method, where we take distance, orientation and semantic similarity of the neighbouring objects into account. Using Machine Learning techniques we obtain corresponding land-use classes. From these a measurement for the semantic distance is derived. It is combined with the orientation difference to generate a matching probability for the two matching candidates. Examples show the benefit of the proposed similarity measure.

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