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SRI International Bioinformatics1
Genome Browser
Tomer Altman
Bioinformatics Research Group
SRI, International
August 19th, 2009
SRI International Bioinformatics2
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
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From Current Organism:
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From Gene Display:
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From Menu:
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The Genome Browser
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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
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Navigation Features
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Browser Diagram
Gene blocks with arrows pointing from 5' to 3'ORFs for proteins have symmetrical arrowheadsRNA genes have asymmetrical arrowheadsPhantom or pseudo-genes are crossed outGenes wrapping around line have 'zig-zag'Genes assigned to transcription unit (TU) are coloredGrey boxes in background also signify TU membershipPromoters and terminators are also displayed
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Browser Legend
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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
displayedAdd External Track
Display GFF file data in context
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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.
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How to Display External Tracks:
Menu: Chromosome -> Select & Browse Chromosome/Replicon
Click “Show Tracks”Menu: Chromosome -> Add External TrackEnter URL or browse local filesCan be repeated multiple times to display several data
sets
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Browser with Tracks Shown
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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
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Genome Omics Viewer
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Comparative Genome Browser
To enter, in Gene page, click on “Align in Multi-Genome Browser”
“Select Allowed Organisms” for what to compare toComparison only works when Ortholog-Links are
presentThe selected gene is centered, and aligned with
Orthologs in the other PGDBsColors mean shared Orthologs. A dozen colors are
reused.
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Comparative Genome Browser Display
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Ortholog-Links
Can be stored as DBLINKS on gene frameshttp://bioinformatics.ai.sri.com/ptools/ortholog-link-
setup.htmlProblem when many PGDBs: grows as N2
Ortholog-Link MySQL DB is used for BioCyc WWW siteContact [email protected] for setup