1. SRI International Bioinformatics 1 Genome Browser Markus Krummenacker Bioinformatics Research Group SRI, International Q2 2013

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 From Current Organism:

4. SRI International Bioinformatics 4 From Menu:

5. SRI International Bioinformatics 5 The Genome Browser

6. SRI International Bioinformatics 6 Browser Navigation The full-length, low-resolution chromosome map is shown at the top, with the selected region in red. A few lines from the selected region are shown below, in higher resolution. Magnification: Click on the top, low-resolution chromosome map Specifying the start & end base-pair positions Entering a gene name Navigation arrows

7. SRI International Bioinformatics 7 Navigation Features

8. SRI International Bioinformatics 8 Browser Diagram 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

9. SRI International Bioinformatics 9 Browser Legend

10. SRI International Bioinformatics 10 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 context

11. SRI International Bioinformatics 11 Displaying External Tracks on the Genome Browser External tracks can be displayed on a chromosome region using the GFF, version 2, file format Flexible format can display 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.

12. SRI International Bioinformatics 12 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

13. SRI International Bioinformatics 13 Browser with Tracks Shown

14. SRI International Bioinformatics 14 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 a given replicon It can also be used to display high-throughput biological experiment data as one of Pathway Tools' Omics Viewers

15. SRI International Bioinformatics 15 Genome Omics Viewer

16. SRI International Bioinformatics 16 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.

17. SRI International Bioinformatics 17 Comparative Genome Browser Display

18. SRI International Bioinformatics 18 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