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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genomic Imprinting and Inheritance02:30

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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What is an Experiment?01:12

What is an Experiment?

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An experiment is a planned activity carried out under controlled conditions. The purpose of an experiment is to investigate the relationship between two variables. When one variable causes change in another, we call the first variable the explanatory or independent variable. The affected variable is called the response or dependent variable. In a randomized experiment, the researcher manipulates values of the explanatory variable and measures the resulting changes in the response variable. The...
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Related Experiment Video

Updated: Jan 28, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Ultra-long Read Sequencing for Whole Genomic DNA Analysis

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svist4get: a simple visualization tool for genomic tracks from sequencing experiments.

Artyom A Egorov1,2, Ekaterina A Sakharova3, Aleksandra S Anisimova4,5

  • 1Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, Moscow, 119234, Russia. artyom.egorov@hotmail.com.

BMC Bioinformatics
|March 8, 2019
PubMed
Summary

svist4get is a new command-line tool that generates publication-quality figures from genomic signal tracks. This bioinformatics tool aids in visualizing Ribo-Seq and RNA-Seq data for automated analysis.

Keywords:
Genome browserGenomic tracksHigh-throughput sequencingNext-generation sequencingPythonRNA-SeqRibo-SeqVisualization

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • High-throughput sequencing generates genomic signal tracks essential for life science research.
  • Existing visualization tools often lack command-line functionality for automated or publication-quality outputs.

Purpose of the Study:

  • To introduce svist4get, a command-line tool for creating publication-ready figures from genomic signal tracks.
  • To enable automated generation of visualizations for bioinformatics pipelines.

Main Methods:

  • svist4get visualizes genomic signal tracks and transcriptome annotations at specified locations.
  • It supports data aggregation from multiple tracks onto a single plot.
  • Outputs can be saved as vector or high-resolution bitmap images.

Main Results:

  • svist4get provides customizable, publication-quality figure generation from genomic signal tracks.
  • Demonstrated utility for visualizing Ribo-Seq and RNA-Seq data.
  • The tool integrates seamlessly into console-based bioinformatics workflows.

Conclusions:

  • svist4get is a Python 3 command-line tool for Linux, facilitating automated bioinformatics analysis.
  • Offers extensive customization via configuration files and a Python API.
  • Available as a PyPI package with source code accessible online.