1. SRI International Bioinformatics 1 Genome Browser Markus Krummenacker Bioinformatics Research Group SRI, International Q3 2015

2. SRI International Bioinformatics 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

3. SRI International Bioinformatics 3 The Genome Browser

4. SRI International Bioinformatics 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

5. SRI International Bioinformatics 5 Navigation Features

6. SRI International Bioinformatics 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)

7. SRI International Bioinformatics 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

8. SRI International Bioinformatics 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.

9. SRI International Bioinformatics 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

10. SRI International Bioinformatics 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

11. SRI International Bioinformatics 11 Browser showing External Track

12. SRI International Bioinformatics 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

13. SRI International Bioinformatics 13 Genome Omics Viewer

14. SRI International Bioinformatics 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.

15. SRI International Bioinformatics 15 Comparative Genome Browser Display

16. SRI International Bioinformatics 16 Ortholog-Links Ortholog-Link MySQL DB is used for BioCyc WWW site Get-Orthologs-From-SRI parameter in ptools-init.dat http://bioinformatics.ai.sri.com/ptools/ortholog-link- setup.html Contact ptools-support@ai.sri.com for setup