1. Bioinformatics Research Group
Genome Browser
Markus Krummenacker
Bioinformatics Research Group
SRI, International
Q1 2017 1 1 1

2. Navigator Genome Browser
The Pathway Tools Navigator allows you to browse the replicons (chromosomes or plasmids) of your PGDB.
Can be accessed a few different ways:
Click on the Replicons or Transcription Units listed on an organism's summary page
Click on the button by the base pair coordinates of a gene display
Menu: Chromosome --> Enter Genome Browser 2 2 2

3. The Genome Browser 3 3 3

4. Browser Navigation
The full-length, low-resolution chromosome map is shown at the top, with the selected region in red.
Several wrapping lines from the selected region are shown below, in higher resolution.
Navigation:
Click on the top, low-resolution chromosome map
Specifying the start & end base-pair positions
Entering a gene name
Navigation arrows 4 4 4

5. Navigation Features 5 5 5

6. Browser Diagram Features
Gene blocks with arrows pointing from 5' to 3'
ORFs for proteins have symmetrical arrowheads
RNA genes have asymmetrical arrowheads
Phantom or pseudo-genes are crossed out
Genes wrapping around line have 'zig-zag'
Genes assigned to transcription unit (TU) are colored
Grey boxes in background also signify TU membership. Greenish = experimental ev.
Promoters and terminators are also displayed
Transcription factor binding sites (red & green) 6 6 6

7. Chromosome Menu Enter Genome Browser For PGDBs with multiple replicons
Show Sequence of a Segment of Chromosome
Sub-sequence of the replicon, or its reverse-compliment
Print Poster
Generate a wall poster-sized PostScript file with the entire genome displayed
Add External Track
Display GFF file data in genome browser context 7 7 7

8. Displaying External Tracks on the Genome Browser
Externally supplied tracks can be displayed on a chromosome region using the GFF, version 2, file format.
A flexible format for displaying various kinds of data: alternate gene predictions, gene expression data, etc.
Each feature line has a start and end position, and optionally a numeric score value. 8 8 8

9. How to Display External Tracks:
Menu: Chromosome -> Enter Genome Browser
Click “Show Tracks”
Menu: Chromosome -> Add External Track
Enter URL or browse local files
Can be repeated multiple times to display several data sets
1 file corresponds to 1 “Track”, but different feature types are grouped together in separate sections 9 9 9

10. Customizing Appearance of External Tracks:
Per-track selector of display style
3 main choices: horizontal, graph, and bar graph
Horizontal: rectangular, colored by the score column
Graph and bar graph: show score in vertical dimension
Bar graphs are filled solidly, to better visualize narrow features
Special syntax in header of GFF file enables assigning a color to all features of the file. E.g. ##color green 10 10 10

11. Browser showing External Track11 11 11

12. The Genome Overview Omics Viewer
The maximum zoom-out level for the Genome Browser is also known as the Genome Overview
You can use the Genome Overview to get a snapshot of the overall gene content for all replicons simultaneously
It can also be used to display high-throughput biological experiment data as one of Pathway Tools' Omics Viewers 12 12 12

13. Genome Omics Viewer 13 13 13

14. Comparative Genome Browser
To enter, in Gene page, click on “Align in Multi- Genome Browser”
“Select Allowed Organisms” for what to compare to
Comparison only works when Ortholog-Links are present
The selected gene is centered, and aligned with Orthologs in the other PGDBs
Colors mean shared Orthologs. A dozen colors are reused. 14 14 14

15. Comparative Genome Browser Display15 15 15

16. Ortholog-Links Ortholog-Link MySQL DB is used for BioCyc WWW site
Get-Orthologs-From-SRI parameter in ptools-init.dat
setup.html
Contact for setup 16 16 16