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Related Concept Videos

Genetic Screens02:46

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 result in visible changes...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Genomics02:02

Genomics

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...
Comparing Copy Number Variations and SNPs02:26

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%...
Genetic Variation01:25

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Related Experiment Video

Updated: May 15, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

M2Viz: a tool for visualizing genetic or proteomic modifications and variants.

Ahmad Rafi1, Alimath Sambreena1, Mahammad Nisar1

  • 1Center for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, 575018, India.

BMC Bioinformatics
|May 14, 2026
PubMed
Summary

M2Viz is a new automated web tool for visualizing mutations and modifications on gene and protein sequences. It supports various omics data types, creating informative lollipop plots for biological insights.

Keywords:
DNA methylationLollipop plotPost-translational modificationSingle amino acid variationsSingle nucleotide variations

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An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci
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An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci

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An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci

Published on: January 25, 2011

Area of Science:

  • Bioinformatics
  • Genomics
  • Proteomics

Background:

  • Visualizing mutations and modifications on nucleotide and protein sequences is crucial for identifying biologically relevant findings from omics data.
  • Lollipop plots are effective for this visualization, allowing for the definition of structural modules to refine mutation/modification patterns.
  • Existing tools often lack automation and are limited in the types of data they can process.

Purpose of the Study:

  • To develop a multi-purpose, open-source, and automated web-based tool for visualizing omics data.
  • To create a user-friendly platform for generating ready-to-use lollipop plots from diverse data inputs.
  • To overcome the limitations of existing tools regarding data compatibility and automation.

Main Methods:

  • Developed M2Viz, a web application with a Python-Django backend, R-based plotting engine, and React.js frontend.
  • Integrated REST API calls to Ensembl and UniProt for automated retrieval of sequence and protein domain information.
  • Enabled end-to-end processing, including data uploading, annotation, and graphical representation.

Main Results:

  • M2Viz visualizes DNA methylation, Single Nucleotide Variations (SNVs), protein Post-Translational Modifications (PTMs), and Single Amino Acid Variations (SAAVs).
  • The tool supports profiling and differential expression/regulation datasets, including numerical data visualization.
  • Automated data retrieval and processing streamline the creation of lollipop plots.

Conclusions:

  • M2Viz is a valuable tool for visualizing DNA methylation, mutational hotspots, and PTMs on gene/protein sequences.
  • The automated visualization pipeline enhances usability across omics pipelines and bioinformatics.
  • M2Viz offers custom plotting flexibility and is freely accessible at https://ciods.in/m2viz.