Bioinformatics Genome Visualization Genomics

Visualization of Genomic Data

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Visualization of Biological Data

Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. Today the Biologists, Biotechnologists, Bioinformaticians and researchers are experiencing a rapid growth in volume and diversity of biological data, presenting an increasing challenge for biologists. A key step in understanding and learning from these data is their visualization. Thus, there has been a corresponding increase in the number and diversity of systems for visualizing biological data.

As a result, keeping an overview of state-of-the-art visualization research has become increasingly challenging for both biology researchers and visualization researchers. To address this challenge, visualization research has been performed for Biosciences and created an interactive web-based visualization tool. These tools help in visualization of sequences, genomes, alignments, phylogenies

macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data.  Visualization of genomic data is frequently employed in biomedical research to access knowledge within a genomic context, to communicate, and to explore datasets for hypothesis generation. This software converts biological data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection.

Tools for Biological data visualization

  • BioVis Explorer allows the exploration of published visualization methods in interactive and intuitive ways
  • BioTapestry, interactive tool for building, visualizing, and simulating genetic regulatory networks
  • VIPER is a visualization tool for exploring inheritance inconsistencies in genotyped pedigrees
  • XiNet is a DataViz tool that allows displaying cross-linking and mass spectrometry results. It generates a cross-link network materialized in the form of node-link diagrams. XiNET allows visualizing positional information, such as linkage sites and linked peptides, at the residue scale.
  • RCSB Protein Data Bank online tool for protein visualization
  • CellVIEW online tool for multiscale large dataset
  • Jalview online tool for visualization of sequence alignments

And the genome browsers used for this purpose are;

  • Ensemble
  • Ucsc
  • NCBI map Viewer

The initial aim of having a genome browser was to display the human genome sequence and provide a platform to allow people to ‘browse’ and analyze the DNA sequence for themselves.

 Ensembl and UCSC use colored and interactive graphics to present the complex data in an integrated manner. The basic structure of the display on many genome browsers is to show the genome sequence horizontally across the screen with certain elements presented in specific colors and shapes according to a key

Each specie has its own page on the browser, which enables you to view and download the DNA sequence and explore other, more specific, information about that genome

Generate Image and Interface

Process Image with Deep Zoom

Generate the HTML, CSS and JavaScript files for the completed DNA Data Visualization interface 

The data is held in data ‘tracks’ which can be switched on and off depending on what aspect of the genome you want to look at

Protein visualization tools are;

  • RasMol 
  • Chime 
  • MolMol 
  • Protein explorer
  • Kinemage Cn3D 

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