scholarly journals MG2C: a user-friendly online tool for drawing genetic maps

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Jiangtao Chao ◽  
Zhiyuan Li ◽  
Yuhe Sun ◽  
Oluwaseun Olayemi Aluko ◽  
Xinru Wu ◽  
...  
Keyword(s):  
Genetic Map ◽  
Recombination Frequency ◽  
Genetic Maps ◽  
Linear Arrangement ◽  
Time Saving ◽  
Online Tool ◽  
Data Output ◽  
Programming Skills ◽  
User Friendly ◽  
Important Basis

AbstractGenetic map is a linear arrangement of the relative positions of sites in the chromosome or genome based on the recombination frequency between genetic markers. It is the important basis for genetic analysis. Several kinds of software have been designed for genetic mapping, but all these tools require users to write or edit code, making it time-costing and difficult for researchers without programming skills to handle with. Here, MG2C, a new online tool was designed, based on PERL and SVG languages.Users can get a standard genetic map, only by providing the location of genes (or quantitative trait loci) and the length of the chromosome, without writing additional code. The operation interface of MG2C contains three sections: data input, data output and parameters. There are 33 attribute parameters in MG2C, which are further divided into 8 modules. Values of the parameters can be changed according to the users’ requirements. The information submitted by users will be transformed into the genetic map in SVG file, which can be further modified by other image processing tools.MG2C is a user-friendly and time-saving online tool for drawing genetic maps, especially for those without programming skills. The tool has been running smoothly since 2015, and updated to version 2.1. It significantly lowers the technical barriers for the users, and provides great convenience for the researchers.

scholarly journals A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

2021 ◽  
pp. 1-7
Author(s):  
Prashant Bhandari ◽  
Tong Geon Lee
Keyword(s):  
Genetic Map ◽  
Recombination Frequency ◽  
Average Distance ◽  
Genetic Research ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphism ◽  
Fresh Market ◽  
Crop Breeding ◽  
Single Nucleotide

Genetic maps saturated with genetic markers are useful for genetic research and crop breeding; however, the genetic map for the large-fruited fresh-market tomato (Solanum lycopersicum) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. We constructed a novel fresh-market tomato genetic map by using 3614 single nucleotide polymorphism (SNP) markers and a 93 F2 segregating progeny derived from a cross between two United States large-fruited fresh-market tomato lines. The average distance between markers was less than 1 cM, and substantial recombination densities between markers were observed across the approximate centromere locations. A linkage panel for large-fruited fresh-market tomato was also established using the combined dataset of the genetic map and 58 SNP-genotyped core tomato lines. The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches.

Prolegomena do tagоwania frazemów w równoległym korpusie rosyjsko-polskim (literatura piękna) w aspekcie przekładoznawczym

2018 ◽  
Vol 2 (XXIII) ◽  
pp. 55-73
Author(s):  
Yury Fedorushkov
Keyword(s):  
Annotation Tool ◽  
Online Tool ◽  
Number Of Factors ◽  
The Status ◽  
Concurrent Objects ◽  
Programming Skills ◽  
User Friendly ◽  
Parallel Texts ◽  
Tagging Methods

This article considers tagging methods for parallel Russian-Polish phrasemathic objects. In particular, an opinion about the annotation tool brat v1.3.is given. This online tool offers a palette of possibilities for classifying words and phrases in parallel texts. Working with this software is largely simplified by a user-friendly interface, and therefore working with the corpus does not cause difficulties for philologists and translators who do not have programming skills. As an example of such a classification, the layout of the metadata system for tagging Russian and Polish parallel phrasemes is described. These resources allow experience to be gathered and concurrent objects to be categorized in the workshop of a translator. As an example, the article presents the tagging of Verb-Noun of the text classified as collocation phrasemes, for example, погасить свет. The status of Verb-Noun constructions is also discussed, which, according to a number of factors, relate to autonomous phrases, although with the status of “free compatibility”, for example, поехать в клуб. A number of recommendations is proposed for the configuration of parallel texts at the level of single sentences.

scholarly journals BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively

2022 ◽  
Vol 12 ◽  
Author(s):  
Kejie Li ◽  
Jessica Hurt ◽  
Christopher D. Whelan ◽  
Ravi Challa ◽  
Dongdong Lin ◽  
...  
Keyword(s):  
High Resolution ◽  
Biological Data ◽  
Web Based ◽  
Online Tool ◽  
Scalable Vector Graphics ◽  
High Resolution Images ◽  
Fit For Purpose ◽  
Programming Skills ◽  
User Friendly ◽  
Publication Quality

Many fit-for-purpose bioinformatics tools generate plots to interpret complex biological data and illustrate findings. However, assembling individual plots in different formats from various sources into one high-resolution figure in the desired layout requires mastery of commercial tools or even programming skills. In addition, it is a time-consuming and sometimes frustrating process even for a computationally savvy scientist who frequently takes a trial-and-error iterative approach to get satisfactory results. To address the challenge, we developed bioInfograph, a web-based tool that allows users to interactively arrange high-resolution images in diversified formats, mainly Scalable Vector Graphics (SVG), to produce one multi-panel publication-quality composite figure in both PDF and HTML formats in a user-friendly manner, requiring no programming skills. It solves stylesheet conflicts of coexisting SVG plots, integrates a rich-text editor, and allows creative design by providing advanced functionalities like image transparency, controlled vertical stacking of plots, versatile image formats, and layout templates. To highlight, the sharable interactive HTML output with zoom-in function is a unique feature not seen in any other similar tools. In the end, we make the online tool publicly available at https://baohongz.github.io/bioInfograph while releasing the source code at https://github.com/baohongz/bioInfograph under MIT open-source license.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

scholarly journals An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 282-295 ◽  
Author(s):  
Elizabeth S Jones ◽  
Natalia L Mahoney ◽  
Michael D Hayward ◽  
Ian P Armstead ◽  
J Gilbert Jones ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Linkage Map ◽  
Genetic Map ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Genetic Linkage Map ◽  
Population Based ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

scholarly journals VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

2020 ◽  
Author(s):  
Jiguang Peng ◽  
Jiale Xiang ◽  
Xiangqian Jin ◽  
Junhua Meng ◽  
Nana Song ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Expert Panel ◽  
Sequence Variant ◽  
Variant Interpretation ◽  
Web Interface ◽  
Online Tool ◽  
Genetic Hearing Loss ◽  
Genetics And Genomics ◽  
Evidence Based Guidelines ◽  
User Friendly

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named VIP-HL, aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants where 83 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

scholarly journals Inferring the number of COVID-19 cases from recently reported deaths

2020 ◽  
Author(s):  
Thibaut Jombart ◽  
Kevin van Zandvoort ◽  
Timothy W Russell ◽  
Christopher I Jarvis ◽  
Amy Gimma ◽  
...  
Keyword(s):  
Contact Tracing ◽  
Online Tool ◽  
Response Strategies ◽  
User Friendly

ABSTRACTWe estimate the number of COVID-19 cases from newly reported deaths in a population without previous reports. Our results suggest that by the time a single death occurs, hundreds to thousands of cases are likely to be present in that population. This suggests containment via contact tracing will be challenging at this point, and other response strategies should be considered. Our approach is implemented in a publicly available, user-friendly, online tool.

scholarly journals AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

2020 ◽  
Author(s):  
Kyle Fletcher ◽  
Lin Zhang ◽  
Juliana Gil ◽  
Rongkui Han ◽  
Keri Cavanaugh ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Map ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

Augmented Reality as a New Media for Supporting Mobile-Learning

2016 ◽  
pp. 655-672
Author(s):  
Mauro Figueiredo ◽  
José Gomes ◽  
Cristina Maria Cardoso Gomes ◽  
Rui Gaspar ◽  
João Madeira Lopes
Keyword(s):  
Augmented Reality ◽  
New Media ◽  
Mobile Device ◽  
Mobile Technologies ◽  
Supplementary Information ◽  
Educational Activities ◽  
Teaching Activities ◽  
Teachers And Students ◽  
Programming Skills ◽  
User Friendly

Combining mobile technologies with Augmented Reality (AR) has recently enabled the ubiquity of AR technologies in our everyday life. We believe that the use of augmented reality will change significantly the teaching activities by enabling the addition of supplementary information that is seen on a mobile device. This chapter presents the most popular augmented reality applications and we select AR eco-systems to be used in daily teaching activities which are user friendly, do not require programming skills and are free. Different augmented reality technologies are explored in this chapter. It is presented the creation of two novel augmented reality books. One developed with teachers and students. Another book that was developed for increasing the interest of reading for children that is being used by storytellers. Several examples are also presented that are used in educational activities, from kindergarten, elementary, secondary schools and university, to improve reading, comprehension, learning of music and better understand the drawing of orthographic views.

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