Genome Map

Overview

Genome Map represents the genome in traditional genome browser layout, where genomic features (i.e. genes) are displayed with boxes around linear chromosome laid out continuously in stacked rows. Local nucleotide content is shown as graphs (A: red, T: green, G: yellow, C: Blue), and CDS are marked with blue stripes, tRNA with green stripes, and rRNA with red stripes. All objects (CDS, tRNA, rRNA) are clickable to display more information. Objects shown above the colored lines are genes on direct strand, and those below are in complementary strands. Overlay of predicted gene expression data is also available.

GenomeMap Close-up

This view is useful to see the lengths and neighboring of genes, possibly forming operons (polycistrons) that are transcribed together as a single mRNA. Neighboring genes are thus likely to have similar functions. Bacterial genomes are highly compact, and therefore large percentage of genes are also overlapped.

Displayed Objects

genes

Three features are displayed in the genome map view: CDS with blue stripes, rRNA with red strpies, and tRNA with green stripes. Gene names are labled at left side of the stripes, corresponding to the 5'-end of genes located in the direct strand (that are located above the color dotted lines, and to the 3'-end of complement genes located below the line.

All gene boxes can be clicked to show detailed annotation.

Genes and RNAs

In many bacterial genomes, genes are preferentially located on the leading strand. Therefore, genomes with highly skewed architecture in this respect have continuous strand preference which reverses in two halves of the genome. tRNA genes are often transcribed together as operons, therefore clustering of green stripes can be found in many bacterial genomes. Operons usually have same name for first three letters of gene names.

nucleotide content

At maximum zoom level, the line representing the chromosome (the horizontal line in the middle in the following image) is composed of colored pixels showing the actual nucleotide sequences. In most bacterial genomes, each pixel represents a single base, but in large genomes, each pixel may represent the most frequent base among several bases. Above the line is a graph of averaged nucleotide content visualized like chromatograms.

Here, A is shown in Red, T is green, G is yellow, and C is blue.

Nucleotide Content

Overlay: gene expression level

Similar to the hybrid satellite map in Google Maps, semi-transparent layers can be overlaid upon the Genome Map View, which can be toggled with buttons located in the upper-right corner. In Genome Projector, overlay for Genome Map shows the predicted gene expression levels calculated using the Codon Adaptation Index. ("The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.", Sharp PM, Li WH., NAR 1987)

Codon Adaptation Index (CAI) measures the relative adaptiveness of the synonymous codon usage bias of a gene towards that of the highly expressed genes, usually using the ribosomal protein-coding genes as reference set. CAI ranges from 0 to 1, that are represented by red to green, respectively.

Overlay

Displayed Annotations

Upon searching, search results are shown as pins on the map, or as text shown in collapsible window on the right-most side. Clicking on each of the pins or text result entries will bring up a dialogue baloon, which shows the following information:

  • gene name
  • product description
  • Gene Ontology terms if available
  • 3D structure if PDB entry was found
  • Links to UniProt, KEGG, NCBI RefSeq, and PDB (if link was found)

In Genome Map View, all features (gene, tRNA, and rRNA) are clickable even without the pins that are only shown when searched.

Annotations

genome_map_view.txt · Last modified: 2009/04/19 15:41 (external edit)