Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes

2020 ◽  
Vol 111 (5) ◽  
pp. 486-490
Author(s):  
Manmohan Pandey ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
Prachi Srivastava ◽  
Suman Saroj ◽  
...  
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Web Browser ◽  
Web Based ◽  
Specific Data ◽  
Sequencing Technologies ◽  
Assembly Algorithms ◽  
User Friendly ◽  
Research Domains ◽  
Generation Sequencing

Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

scholarly journals ELIMU-MDx: a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data

BioTechniques ◽  
2020 ◽  
Vol 68 (1) ◽  
pp. 22-27 ◽  
Author(s):  
Silvan Krähenbühl ◽  
Fabian Studer ◽  
Etienne Guirou ◽  
Anna Deal ◽  
Philipp Mächler ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Turnaround Time ◽  
Storage Management ◽  
Quantitative Real Time Pcr ◽  
Web Browser ◽  
Web Based ◽  
Data Standard ◽  
User Friendly

The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a user-friendly platform designed and built to accelerate the turnaround time of diagnostic qPCR assays. ELIMU-MDx is compliant with Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines and has extensive data-import capabilities for all major qPCR instruments by using the RDML data standard. This platform was designed as an open-source software tool and can be accessed through the web browser on all major operating systems.

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

scholarly journals Interactive Web-Based Resource for Annotation of Genetic Variants Causing Hereditary Angioedema (HADA): Database Development, Implementation, and Validation (Preprint)

2020 ◽  
Author(s):  
Alejandro Mendoza-Alvarez ◽  
Adrián Muñoz-Barrera ◽  
Luis Alberto Rubio-Rodríguez ◽  
Itahisa Marcelino-Rodriguez ◽  
Almudena Corrales ◽  
...  
Keyword(s):  
Hereditary Angioedema ◽  
Genetic Condition ◽  
First Line ◽  
International Consensus ◽  
Web Based ◽  
Genetics And Genomics ◽  
User Friendly ◽  
Current Guidelines ◽  
Generation Sequencing ◽  
Esterase Inhibitor

BACKGROUND Hereditary angioedema is a rare genetic condition caused by C1 esterase inhibitor deficiency, dysfunction, or kinin cascade dysregulation, leading to an increased bradykinin plasma concentration. Hereditary angioedema is a poorly recognized clinical entity and is very often misdiagnosed as a histaminergic angioedema. Despite its genetic nature, first-line genetic screening is not integrated in routine diagnosis. Consequently, a delay in the diagnosis, and inaccurate or incomplete diagnosis and treatment of hereditary angioedema are common. OBJECTIVE In agreement with recent recommendations from the International Consensus on the Use of Genetics in the Management of Hereditary Angioedema, to facilitate the clinical diagnosis and adapt it to the paradigm of precision medicine and next-generation sequencing–based genetic tests, we aimed to develop a genetic annotation tool, termed Hereditary Angioedema Database Annotation (HADA). METHODS HADA is built on top of a database of known variants affecting function, including precomputed pathogenic assessment of each variant and a ranked classification according to the current guidelines from the American College of Medical Genetics and Genomics. RESULTS HADA is provided as a freely accessible, user-friendly web-based interface with versatility for the entry of genetic information. The underlying database can also be incorporated into automated command-line stand-alone annotation tools. CONCLUSIONS HADA can achieve the rapid detection of variants affecting function for different hereditary angioedema types, and further integrates useful information to reduce the diagnosis odyssey and improve its delay.

Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology

Weed Science ◽  
2009 ◽  
Vol 57 (5) ◽  
pp. 463-469 ◽  
Author(s):  
Ryan M. Lee ◽  
Jyothi Thimmapuram ◽  
Kate A. Thinglum ◽  
George Gong ◽  
Alvaro G. Hernandez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Ecological Model ◽  
Average Length ◽  
Science Research ◽  
Complete Sequence ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Sequencing Technologies ◽  
Generation Sequencing

Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.

scholarly journals Next-Generation Sequencing Technologies in Blood Group Typing

2019 ◽  
Vol 47 (1) ◽  
pp. 4-13 ◽  
Author(s):  
Daniel Fürst ◽  
Chrysanthi Tsamadou ◽  
Christine Neuchel ◽  
Hubert Schrezenmeier ◽  
Joannis Mytilineos ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Blood Group ◽  
Large Scale ◽  
Cost Effective ◽  
Molecular Testing ◽  
Blood Group Antigens ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Blood Group Typing ◽  
Generation Sequencing

Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.

lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics

2016 ◽  
Vol 14 (04) ◽  
pp. 1650016 ◽  
Author(s):  
Ruifeng Hu ◽  
Xiaobo Sun
Keyword(s):  
Free Energy ◽  
Nucleic Acid ◽  
Large Scale ◽  
Nearest Neighbor ◽  
Binding Free Energy ◽  
Target Prediction ◽  
Easy Access ◽  
Web Based ◽  
Size Limitation ◽  
User Friendly

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

scholarly journals Discovery research to clinical trial: A ten year journey

2010 ◽  
Vol 33 (6) ◽  
pp. 342 ◽  
Author(s):  
Torsten O Nielsen
Keyword(s):  
Large Scale ◽  
Clinical Care ◽  
Young Investigator ◽  
Giant Cell Tumors ◽  
The Road ◽  
Sequencing Technologies ◽  
Discovery Research ◽  
Deacetylase Inhibitor ◽  
Impact Patient Care ◽  
Generation Sequencing

Clinician-scientists have the training and motivation to translate basic science into tools for improved clinical care, but the road to achieve this is hardly straight forward, particularly for large scale genomic datasets. This year’s Joe Doupe Young Investigator award winner, Dr. Torsten Nielsen, details successful examples of new scientific insights, diagnostics and clinical trials that have resulted from microarray-based gene expression profiling of sarcomas: TLE1 as a biomarker for synovial sarcoma, histone deacetylase inhibitor therapy for translocation-associated sarcomas of young adults, and CSF1 pathway inhibitors for tenosynovial giant cell tumors. Results from exciting, emerging next generation sequencing technologies will need to undergo similar validation and preclinical studies before they can be expected to impact patient care.

scholarly journals Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

2016 ◽  
Author(s):  
Po-E Li ◽  
Chien-Chi Lo ◽  
Joseph J. Anderson ◽  
Karen W. Davenport ◽  
Kimberly A. Bishop-Lilly ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Initial Attempt ◽  
Web Based ◽  
Fully Integrated ◽  
Sequencing Technologies ◽  
Number Of Factors ◽  
Wide Range ◽  
Flood Current ◽  
Wide Assortment ◽  
Generation Sequencing

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools. These preconfigured workflows provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks, and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications.

scholarly journals RaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffraction

2020 ◽  
Vol 53 (2) ◽  
pp. 587-593
Author(s):  
A. Boulle ◽  
V. Mergnac
Keyword(s):  
Web Application ◽  
The Internet ◽  
Programming Environment ◽  
X Ray Diffraction ◽  
Web Browser ◽  
Web Based ◽  
X Ray ◽  
Depth Profiles ◽  
User Friendly

RaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst. 49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.

scholarly journals The Framework for Web-Based Automated Online Question Paper Generator through JEE

2018 ◽  
Vol 7 (3) ◽  
pp. 1415
Author(s):  
Vinayak Hegde ◽  
Lavanya V Rao ◽  
Shivali B S
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Educational Institution ◽  
Faculty Members ◽  
Educational Institutions ◽  
Small Scale ◽  
Web Based ◽  
Educational Institute ◽  
User Friendly ◽  
Word Format

Examinations are an indispensable part of a student’s life. In the conventional mechanism, the question paper generation is time-consuming work for the faculty members of the educational institution. Every educational institute mandatorily expects exam setters to follow its own typesetting format. We have designed the automated question paper setting software to be user-friendly so that, paper setters can overcome from the typographic problem. Presently in most of the educational institutions question papers are set manually. It is time-consuming work and there may be chances of repetition of the same questions. So, in order to make the question paper generation more convenient to use, the web application is developed using Java Enterprise Edition (JEE) that can be accessed from LAN/Intranet.The application comes with the Admin Module and Teachers Module. The Admin grants access to the users by registering them. The faculty can access the system once they are registered. The faculty can enter questions in the database daily as per their free time. In this way, the question pool can be generated. The questions are approved by the chairperson and substandard questions are discarded. The question paper is then generated by selected course experts. The Fisher-Yates Shuffling algorithm used to choose questions randomly from the pool of questions from the database. Text Mining Algorithm aids in duplicity removal from the paper.  The generated question paper will be in Word Format. In our application, we assure better security, removal of duplicity, cost-effectiveness, and human intervention avoidance. It can be used by small-scale and large-scale institutions.  

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