scholarly journals AliTV—interactive visualization of whole genome comparisons

2017 ◽  
Vol 3 ◽  
pp. e116 ◽  
Author(s):  
Markus J. Ankenbrand ◽  
Sonja Hohlfeld ◽  
Thomas Hackl ◽  
Frank Förster
Keyword(s):  
Comparative Analysis ◽  
Genome Evolution ◽  
Genetic Information ◽  
Interactive Visualization ◽  
Whole Genome ◽  
High Quality ◽  
Web Browser ◽  
User Friendly ◽  
Genome Comparisons ◽  
Initial Results

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation of the initial results. Limitations of existing software inspired us to develop our new tool AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV.

scholarly journals AliTV-interactive visualization of whole genome comparisons

2016 ◽  
Author(s):  
Markus J. Ankenbrand ◽  
Sonja Hohlfeld ◽  
Thomas Hackl ◽  
Frank Förster
Keyword(s):  
Comparative Analysis ◽  
Genome Evolution ◽  
Genetic Information ◽  
Interactive Visualization ◽  
Whole Genome ◽  
High Quality ◽  
Web Browser ◽  
User Friendly ◽  
Genome Comparisons ◽  
Initial Results

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation of the initial results. Limitations of existing software inspired us to develop our new tool AliTV, which provides interac- tive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV.

scholarly journals AliTV-interactive visualization of whole genome comparisons

2017 ◽  
Author(s):  
Markus J. Ankenbrand ◽  
Sonja Hohlfeld ◽  
Thomas Hackl ◽  
Frank Förster
Keyword(s):  
Comparative Analysis ◽  
Genome Evolution ◽  
Genetic Information ◽  
Interactive Visualization ◽  
Whole Genome ◽  
High Quality ◽  
Web Browser ◽  
User Friendly ◽  
Genome Comparisons ◽  
Initial Results

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation of the initial results. Limitations of existing software inspired us to develop our new tool AliTV, which provides interac- tive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV.

scholarly journals AliTV-interactive visualization of whole genome comparisons

2017 ◽  
Author(s):  
Markus J. Ankenbrand ◽  
Sonja Hohlfeld ◽  
Thomas Hackl ◽  
Frank Förster
Keyword(s):  
Comparative Analysis ◽  
Genome Evolution ◽  
Genetic Information ◽  
Interactive Visualization ◽  
Whole Genome ◽  
High Quality ◽  
Web Browser ◽  
User Friendly ◽  
Genome Comparisons ◽  
Initial Results

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation of the initial results. Limitations of existing software inspired us to develop our new tool AliTV, which provides interac- tive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV.

scholarly journals GenomeGraphR: A user-friendly open-source web application for foodborne pathogen Whole Genome Sequencing data integration, analysis, and visualization.

2018 ◽  
Author(s):  
Moez Sanaa ◽  
Régis Pouillot ◽  
Francisco J Garces-Vega ◽  
Errol Strain ◽  
Jane M Van Doren
Keyword(s):  
Genome Sequencing ◽  
Pathogen Detection ◽  
Foodborne Pathogen ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
High Quality ◽  
User Friendly ◽  
Integration Analysis

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/genomegraphr/).

Qualitative anatomical restoration of the contact point of teeth – prevention of localized forms of periodontal diseases

2020 ◽  
Vol 25 (1) ◽  
pp. 10-15
Author(s):  
L. Yu. Orekhova ◽  
O. V. Prokhorova ◽  
V. Yu. Shefov
Keyword(s):  
Comparative Analysis ◽  
Computer Simulations ◽  
Periodontal Diseases ◽  
Contact Point ◽  
Clinical Stage ◽  
High Quality ◽  
Cross Sectional ◽  
Clinical Stages ◽  
Anatomical Restoration ◽  
Approximal Surfaces

Relevance. The restoration of a high-quality anatomical and functional contact point of teeth plays an important role in preventing the development of localized forms of periodontal disease.Purpose. Development of recommendations for qualitative anatomical restoration of the contact point of teeth for the prevention of localized forms of periodontal diseases.Materials and methods. In our study, which consisted of pre-clinical and clinical stages, were analyzed 50 CT scan of the chewing group teeth calculated the ratio of approximal surfaces of molars and premolars to the width of their crowns and computer simulations of the results of restoration of contact point. We also conducted a comparative analysis of wedges of different material with different cross-sectional shapes. At the clinical stage, the restoration of the contact point of teeth in patients according to our recommendations was carried out.Results. On the basis of the data obtained during the study, a formula for calculating the height and size of the restored contact point was compiled. Recommendations for anatomical restoration of the contact point are formulated.Conclusion. The application of the recommendations developed by us allows anatomically qualitatively restore the contact point and prevent the development of localized periodontal diseases.

A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

2021 ◽  
Author(s):  
Yi‐Ming Weng ◽  
Charlotte B. Francoeur ◽  
Cameron R. Currie ◽  
David H. Kavanaugh ◽  
Sean D. Schoville
Keyword(s):  
Genome Evolution ◽  
Genome Assembly ◽  
Cold Adaptation ◽  
High Quality

scholarly journals Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gareth B. Gillard ◽  
Lars Grønvold ◽  
Line L. Røsæg ◽  
Matilde Mengkrog Holen ◽  
Øystein Monsen ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Whole Genome Duplication ◽  
Genome Stability ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Whole Genome ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Doubling ◽  
Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

scholarly journals Prioritising recommendations following analyses of adverse events in healthcare: a systematic review

2020 ◽  
Vol 9 (4) ◽  
pp. e000843
Author(s):  
Kelly Bos ◽  
Maarten J van der Laan ◽  
Dave A Dongelmans
Keyword(s):  
Systematic Review ◽  
Adverse Events ◽  
Data Extraction ◽  
Data Sources ◽  
Cochrane Library ◽  
High Quality ◽  
Data Synthesis ◽  
Study Selection ◽  
Personal Opinion ◽  
User Friendly

PurposeThe purpose of this systematic review was to identify an appropriate method—a user-friendly and validated method—that prioritises recommendations following analyses of adverse events (AEs) based on objective features.Data sourcesThe electronic databases PubMed/MEDLINE, Embase (Ovid), Cochrane Library, PsycINFO (Ovid) and ERIC (Ovid) were searched.Study selectionStudies were considered eligible when reporting on methods to prioritise recommendations.Data extractionTwo teams of reviewers performed the data extraction which was defined prior to this phase.Results of data synthesisEleven methods were identified that are designed to prioritise recommendations. After completing the data extraction, none of the methods met all the predefined criteria. Nine methods were considered user-friendly. One study validated the developed method. Five methods prioritised recommendations based on objective features, not affected by personal opinion or knowledge and expected to be reproducible by different users.ConclusionThere are several methods available to prioritise recommendations following analyses of AEs. All these methods can be used to discuss and select recommendations for implementation. None of the methods is a user-friendly and validated method that prioritises recommendations based on objective features. Although there are possibilities to further improve their features, the ‘Typology of safety functions’ by de Dianous and Fiévez, and the ‘Hierarchy of hazard controls’ by McCaughan have the most potential to select high-quality recommendations as they have only a few clearly defined categories in a well-arranged ordinal sequence.

scholarly journals Numerical Analysis on Performance of the Middle-Pressure Jet Grouting Method for Ground Improvement

Geosciences ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 313
Author(s):  
Shinya Inazumi ◽  
Sudip Shakya ◽  
Takahiro Komaki ◽  
Yasuharu Nakanishi
Keyword(s):  
Life Cycle ◽  
Comparative Analysis ◽  
Ground Improvement ◽  
Cement Slurry ◽  
Mechanical Agitation ◽  
High Quality ◽  
Jet Grouting ◽  
Computer Aided ◽  
Improvement Method ◽  
Cae System

This study focused on the middle-pressure jet grouting method, which has a complicated development mechanism for the columnar soil-improved body, with the aim of establishing a computer-aided engineering (CAE) system that can simulate the performance on a computer. Furthermore, in order to confirm the effect of middle-pressure jet grouting with mechanical agitation and mixing, a comparative analysis was performed with different jet pressures, the development situation was visualized, and the performance of this method was evaluated. The results of MPS-CAE as one of the CAE systems showed that the cement slurry jet ratio in the planned improvement range, including the periphery of the mixing blade, by the middle-pressure jet grouting together with the mechanical agitation and mixing was increased and a high quality columnar soil-improved body was obtained. It is expected that the introduction of CAE will contribute to the visualization of the ground, and that CAE will be an effective tool for the visual management of construction for ground improvement and the maintenance of improved grounds during the life cycle of the ground-improvement method.

scholarly journals BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology

iScience ◽  
2020 ◽  
Vol 23 (1) ◽  
pp. 100769 ◽  
Author(s):  
Basil B. Xavier ◽  
Mohamed Mysara ◽  
Mattia Bolzan ◽  
Bruno Ribeiro-Gonçalves ◽  
Blaise T.F. Alako ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Clinical Diagnostic ◽  
User Friendly
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