Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genetic Screens

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...

Modified Boxplots

Modified Boxplots

A standard box and whisker plot informs us about the spread of the data in a given sample. One can identify the minimum value, maximum value, first quartile value, second quartile or median value, and third quartile.
However, the box plot does not tell the reader about outliers - values that lie far from the center of the data. We can modify the standard box and whisker plot to identify the outliers and visualize the actual spread of the data in a sample.
Initially, we calculate the adjusted...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

Residual Plots

Residual Plots

A residual plot is a statistical representation of data used to analyze correlation and regression results. It helps verify the requirements for drawing specific conclusions about correlation and regression. To obtain the residual plot, first, the residual for each data value is calculated, which is simply the vertical distance between the observed and the predicted value obtained from the regression equation.
When the residual values are plotted against the variable x, it is called a residual...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Genome Copying Errors

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Transcription initiation drives dosage compensation establishment and maintenance in male <i>Drosophila</i>.

Science advances·2026

Same author

Enhanced IGFL1 translation in response to IL-1β is controlled by distinct 3'UTR elements.

PloS one·2026

Same author

LiraSearch-ultrafast ligand shape and electrostatic matching server.

Bioinformatics advances·2026

Same author

Autoencoder/RandomForest-TabPFN for cross-cancer metabolomics: prostate and breast cancer diagnosis using paper spray and ion mobility-mass spectrometry techniques.

GigaScience·2026

Same author

A leader-repeat hairpin blocks extraneous CRISPR RNA production in diverse CRISPR-Cas13 systems.

The EMBO journal·2026

Same author

Ten common misconceptions about Galaxy (and why they are wrong!).

PLoS computational biology·2026

Search research articles

Related Experiment Video

Updated: Dec 13, 2025

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

Published on: September 16, 2019

pyGenomeTracks: reproducible plots for multivariate genomic datasets.

Lucille Lopez-Delisle¹, Leily Rabbani², Joachim Wolff³

¹UPDUB, ISREC Department, School of Life Sciences (SV), EPFL, 1015 Lausanne, Switzerland.

Bioinformatics (Oxford, England)

|August 4, 2020

Summary

Generating publication-ready genomic track plots is challenging. pyGenomeTracks (PGT) offers a reproducible and customizable solution for creating complex figures efficiently.

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Related Experiment Videos

Last Updated: Dec 13, 2025

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

Published on: September 16, 2019

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Generating publication-quality figures for multiple genomic tracks is complex and time-consuming.
Manual figure creation or reliance on vector graphics software requires significant effort and expertise.

Purpose of the Study:

To introduce pyGenomeTracks (PGT) as a modular tool for simplifying the generation of genomic track plots.
To enable reproducible and standardized creation of customizable, publication-ready genomic visualizations.

Main Methods:

PGT is a modular plotting tool designed for combining multiple genomic tracks.
The tool facilitates the generation of highly customizable and publication-ready images.

Main Results:

pyGenomeTracks enables the easy combination of multiple genomic tracks.
It supports reproducible and standardized generation of complex figures.

Conclusions:

PGT simplifies the creation of publication-ready genomic track plots.
The tool enhances reproducibility and customization in genomic data visualization.