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Genome Browser Navigation and Features | SRI Bioinformatics Research Group

Explore replicons of your PGDB through Genome Browser Navigation. View chromosome maps, gene features, external tracks, and compare genomes with Ortholog-Links. Utilize various tools for comprehensive genome analysis.

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Genome Browser Navigation and Features | SRI Bioinformatics Research Group

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

  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. The Genome Browser

  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. Navigation Features

  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. 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. 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. 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. Customizing Appearance ofExternal 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. Browser showing External Track

  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. Genome Omics Viewer

  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. Comparative Genome Browser Display

  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

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