1. SRI International Bioinformatics 1 Genome Browser Tomer Altman Bioinformatics Research Group SRI, International August 19th, 2009

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 replicon or Transcription Units listed on a single organism display Click on the base pair coordinates of a gene display Menu: Chromosome --> Select & Browse Chromosome/Replicon

3. SRI International Bioinformatics 3 From Current Organism:

4. SRI International Bioinformatics 4 From Gene Display:

5. SRI International Bioinformatics 5 From Menu:

6. SRI International Bioinformatics 6 The Genome Browser

7. SRI International Bioinformatics 7 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

8. SRI International Bioinformatics 8 Navigation Features

9. SRI International Bioinformatics 9 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 Promoters and terminators are also displayed

10. SRI International Bioinformatics 10 Browser Legend

11. SRI International Bioinformatics 11 Chromosome Menu Select & Browse Chromosome/Replicon 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

12. SRI International Bioinformatics 12 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.

13. SRI International Bioinformatics 13 How to Display External Tracks: Menu: Chromosome -> Select & Browse Chromosome/Replicon Click “Show Tracks” Menu: Chromosome -> Add External Track Enter URL or browse local files Can be repeated multiple times to display several data sets

14. SRI International Bioinformatics 14 Browser with Tracks Shown

15. SRI International Bioinformatics 15 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

16. SRI International Bioinformatics 16 Genome Omics Viewer

17. SRI International Bioinformatics 17 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.

18. SRI International Bioinformatics 18 Comparative Genome Browser Display

19. SRI International Bioinformatics 19 Ortholog-Links Can be stored as DBLINKS on gene frames http://bioinformatics.ai.sri.com/ptools/ortholog-link- setup.html Problem when many PGDBs: grows as N 2 Ortholog-Link MySQL DB is used for BioCyc WWW site Contact ptools-support@ai.sri.com for setupptools-support@ai.sri.com