KOnezumi: a web application for automating gene disruption strategies to generate knockout mice

Abstract Summary Although gene editing using the CRISPR/Cas9 system enables the rapid generation of knockout mice, constructing an optimal gene disruption strategy is still labourious. Here, we propose KOnezumi, a simple and user-friendly web application, for use in automating the design of knockout strategies for multiple genes. Users only need to input gene symbols, and then KOnezumi returns target exons, gRNA candidates to delete the target exons, genotyping PCR primers, nucleotide sequences of the target exons and coding sequences of expected deletion products. KOnezumi enables users to easily and rapidly apply a rational strategy to accelerate the generation of KO mice using the CRISPR/Cas9 system. Availability and implementation This web application is freely available at http://www.md.tsukuba.ac.jp/LabAnimalResCNT/KOanimals/konezumi.html. Supplementary information Supplementary data are available at Bioinformatics online.

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PathScore: a web tool for identifying altered pathways in cancer data

10.1101/067090 ◽

2016 ◽

Cited By ~ 2

Author(s):

Stephen G. Gaffney ◽

Jeffrey P. Townsend

Keyword(s):

Web Application ◽

Somatic Mutations ◽

Supplementary Information ◽

Web Tool ◽

Cancer Data ◽

Link Type ◽

Novel Approach ◽

Supplementary Material ◽

User Friendly ◽

Pathway Effect

ABSTRACTSummaryPathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.Availability and ImplementationWeb application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at github.com/sggaffney/pathscore with a GPLv3 [email protected] InformationAdditional documentation can be found at http://pathscore.publichealth.yale.edu/faq.

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YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells

Bioinformatics ◽

10.1093/bioinformatics/btz402 ◽

2019 ◽

Vol 35 (21) ◽

pp. 4525-4527 ◽

Cited By ~ 10

Author(s):

Alex X Lu ◽

Taraneh Zarin ◽

Ian S Hsu ◽

Alan M Moses

Keyword(s):

Image Analysis ◽

Web Application ◽

Single Cells ◽

Yeast Cells ◽

Supplementary Information ◽

Supplementary Data ◽

User Friendly ◽

Microscopy Images

Abstract Summary We introduce YeastSpotter, a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines. Availability and implementation YeastSpotter is available at http://yeastspotter.csb.utoronto.ca/. Code is available at https://github.com/alexxijielu/yeast_segmentation. Supplementary information Supplementary data are available at Bioinformatics online.

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DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity

Bioinformatics ◽

10.1093/bioinformatics/btz834 ◽

2019 ◽

Cited By ~ 2

Author(s):

Matthew Carlucci ◽

Algimantas Kriščiūnas ◽

Haohan Li ◽

Povilas Gibas ◽

Karolis Koncevičius ◽

...

Keyword(s):

Web Application ◽

Statistical Significance ◽

R Package ◽

Biological Data ◽

Supplementary Information ◽

Statistical Knowledge ◽

Health And Disease ◽

Phase Amplitude ◽

Almost All ◽

User Friendly

Abstract Motivation Biological rhythmicity is fundamental to almost all organisms on Earth and plays a key role in health and disease. Identification of oscillating signals could lead to novel biological insights, yet its investigation is impeded by the extensive computational and statistical knowledge required to perform such analysis. Results To address this issue, we present DiscoRhythm (Discovering Rhythmicity), a user-friendly application for characterizing rhythmicity in temporal biological data. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). We optimized these algorithms for speed, improving their execution times up to 30-fold to enable rapid analysis of -omic-scale datasets in real-time. Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity. Availability and Implementation The DiscoRhythm R package is available on Bioconductor (https://bioconductor.org/packages/DiscoRhythm), with source code available on GitHub (https://github.com/matthewcarlucci/DiscoRhythm) under a GPL-3 license. The web application is securely deployed over HTTPS (https://disco.camh.ca) and is freely available for use worldwide. Local instances of the DiscoRhythm web application can be created using the R package or by deploying the publicly available Docker container (https://hub.docker.com/r/mcarlucci/discorhythm). Supplementary information Supplementary data are available at Bioinformatics online.

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G4Killer web application: a tool to design G-quadruplex mutations

Bioinformatics ◽

10.1093/bioinformatics/btaa057 ◽

2020 ◽

Vol 36 (10) ◽

pp. 3246-3247

Author(s):

Vaclav Brazda ◽

Jan Kolomaznik ◽

Jean-Louis Mergny ◽

Jiri Stastny

Keyword(s):

Dna Sequences ◽

Web Application ◽

Rational Design ◽

Therapeutic Potential ◽

Supplementary Information ◽

Web Tool ◽

Web Based ◽

Dna Structures ◽

G Quadruplex ◽

User Friendly

Abstract Motivation G-quadruplexes (G4) are important regulatory non-B DNA structures with therapeutic potential. A tool for rational design of mutations leading to decreased propensity for G4 formation should be useful in studying G4 functions. Although tools exist for G4 prediction, no easily accessible tool for the rational design of G4 mutations has been available. Results We developed a web-based tool termed G4Killer that is based on the G4Hunter algorithm. This new tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps. Availability and implementation The G4Killer web tool can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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G4Hunter web application: a web server for G-quadruplex prediction

Bioinformatics ◽

10.1093/bioinformatics/btz087 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3493-3495 ◽

Cited By ~ 22

Author(s):

Václav Brázda ◽

Jan Kolomazník ◽

Jiří Lýsek ◽

Martin Bartas ◽

Miroslav Fojta ◽

...

Keyword(s):

Data Storage ◽

Web Application ◽

Data Representation ◽

Complete Characterization ◽

Supplementary Information ◽

Web Based ◽

Rna Molecules ◽

Dna And Rna ◽

Sorting Data ◽

User Friendly

Abstract Motivation Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. Results We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. Availability and implementation G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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Asc-Seurat – Analytical single-cell Seurat-based web application

10.1101/2021.03.19.436196 ◽

2021 ◽

Author(s):

WJ Pereira ◽

FM Almeida ◽

KM Balmant ◽

DC Rodriguez ◽

PM Triozzi ◽

...

Keyword(s):

Single Cell ◽

Web Application ◽

Iterative Process ◽

Developmental Trajectories ◽

Cell Types ◽

Biological Information ◽

Supplementary Information ◽

Popular Approach ◽

Single Cell Rna Sequencing ◽

User Friendly

AbstractSummarySingle-cell RNA sequencing (scRNA-seq) has become a popular approach for studying the transcriptome, providing a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data processing and uncover relevant biological information. We present Asc-Seurat, a feature rich workbench, providing a user-friendly and easy-to-install web application encapsulating the necessary tools for an all-encompassing and fluid scRNA-seq data analysis.Availability and implementationAsc-Seurat is available at https://github.com/KirstLab/asc_seurat/ and released under GNU 3 [email protected] informationSupplementary data are available at Bioinformatics online.

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RAD: a web application to identify region associated differentially expressed genes

Bioinformatics ◽

10.1093/bioinformatics/btab075 ◽

2021 ◽

Author(s):

Yixin Guo ◽

Ziwei Xue ◽

Ruihong Yuan ◽

Jingyi Jessica Li ◽

William A Pastor ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Web Application ◽

Distal Region ◽

Differentially Expressed ◽

Supplementary Information ◽

Regulatory Function ◽

Genome Wide ◽

Wide Scale ◽

Genomic Regions ◽

User Friendly

Abstract Summary With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually less focused, largely due to the lack of reliable tools to link these regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes (DEGs). With DEGs and genomic regions of interest (gROI) as input, RAD maps the up- and down-regulated genes associated with any gROI and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance. Availability and implementation RAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available at https://labw.org/rad as online web service. Supplementary information Supplementary data are available at Bioinformatics online.

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Primer Server - A web application to design primers for the amplification of unique DNA targets in complex genomes

Journal of Student Research ◽

10.47611/jsr.vi.454 ◽

2018 ◽

Author(s):

Takao Shibamoto ◽

Kokulapalan Wimalanathan ◽

Erica Unger-Wallace ◽

Erik Vollbrecht

Keyword(s):

Web Application ◽

Genetic Material ◽

Pcr Primers ◽

Test Tube ◽

Dna Bases ◽

Web Based ◽

User Input ◽

Server Side ◽

Target Binding ◽

User Friendly

Polymerase Chain Reaction (PCR) is one of the most important inventions of the 20th century in molecular biology. PCR is a technique to amplify or make in a test tube many copies of a specific DNA region. Miniscule amounts of the genetic material from any organism can now be amplified to identify individuals, manipulate DNA, detect infectious organisms including the viruses that cause AIDS, hepatitis, and tuberculosis, detect genetic variations including mutations in genes, and numerous other tasks. PCR primers are short, single-stranded DNAs that define the section of DNA to be amplified. Two primers are used in each PCR reaction, designed so that they bind at flanking locations surrounding the target region. Critically, off-target binding may lead to experimental failure or worse, to misleading results. Thus, potential primers of approximately 20 DNA bases in length, must be examined for off-target binding among, for example, the 3.2 billion DNA bases from all human chromosomes, the human genome. The purpose of our study is to make a user-friendly tool (Primer Server) that can design PCR primers efficiently and accurately as well as visualize the designed primers. Our web-based bioinformatics tool selects optimal primer sequences within the starting material by using a C module called primer3 and then prioritizing and/or eliminating potential primers based on comparison of the primer bases against all bases in the genome using an algorithm called BLAST. This tool has an easy-to-use interface which was designed using Angular2, and an efficient server-side code written in Python. While similar tools exist, our tool is more user-friendly, efficient and uses extensive form validation to minimize errors in the user input. Our tool can be used to design primers that will be used in laboratory experiments to amplify DNA from various organisms, including large, complex genomes such as humans, other animals and plants.

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VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects

Bioinformatics ◽

10.1093/bioinformatics/btz458 ◽

2019 ◽

Vol 35 (22) ◽

pp. 4803-4805 ◽

Cited By ~ 1

Author(s):

Raul Ossio ◽

O Isaac Garcia-Salinas ◽

Diego Said Anaya-Mancilla ◽

Jair S Garcia-Sotelo ◽

Luis A Aguilar ◽

...

Keyword(s):

Exome Sequencing ◽

Web Application ◽

Source Code ◽

Supplementary Information ◽

Sequencing Data ◽

Genomic Variants ◽

Exome Sequencing Data ◽

Variant Filtering ◽

Variant Information ◽

User Friendly

Abstract Motivation Identifying disease-causing variants from exome sequencing projects remains a challenging task that often requires bioinformatics expertise. Here we describe a user-friendly graphical application that allows medical professionals and bench biologists to prioritize and visualize genetic variants from human exome sequencing data. Results We have implemented VCF/Plotein, a graphical, fully interactive web application able to display exome sequencing data in VCF format. Gene and variant information is extracted from Ensembl. Cross-referencing with external databases and application-based gene and variant filtering have also been implemented. All data processing is done locally by the user’s CPU to ensure the security of patient data. Availability and implementation Freely available on the web at https://vcfplotein.liigh.unam.mx. Website implemented in JavaScript using the Vue.js framework, with all major browsers supported. Source code freely available for download at https://github.com/raulossio/VCF-plotein. Supplementary information Supplementary data are available at Bioinformatics online.

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Biopipe: A Lightweight System Enabling Comparison of Bioinformatics Tools and Workflows

10.1101/201186 ◽

2017 ◽

Author(s):

Saima Sultana Tithi ◽

Jiyoung Lee ◽

Liqing Zhang ◽

Song Li ◽

Na Meng

Keyword(s):

Web Application ◽

Supplementary Information ◽

Next Generation Sequencing Data ◽

Sequencing Data ◽

Web Interfaces ◽

Link Type ◽

Bioinformatics Tools ◽

Multiple Alternative ◽

Portable System ◽

User Friendly

AbstractAnalyzing next generation sequencing data always requires researchers to install many tools, prepare input data compliant to the required data format, and execute the tools in specific orders. Such tool installation and workflow execution process is tedious and error-prone, and becomes very challenging when researchers need to compare multiple alternative tool chains. To mitigate this problem, we developed a new lightweight and portable system, Biopipe, to simplify the creation and execution of bioinformatics tools and workflows, and to further enable the comparison between alternative tools or workflows. Biopipe allows users to create and edit workflows with user-friendly web interfaces, and automates tool installation as well as workflow synthesis by downloading and executing predefined Docker images. With Biopipe, biologists can easily experiment with and compare different bioinformatics tools and workflows without much computer science knowledge. There are mainly two parts in Biopipe: a web application and a standalone Java application. They are freely available at http://bench.cs.vt.edu:8282/Biopipe-Workflow-Editor-0.0.1/index.xhtml and https://code.vt.edu/saima5/[email protected] informationSupplementary data are available online.

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