Download Genome Browser - Pathway Tools

Genome Browser
Markus Krummenacker
Bioinformatics Research Group
SRI, International
Q2 2013
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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
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From Current Organism:
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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 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
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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
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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 -> 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
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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 MultiGenome 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.
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Comparative Genome Browser
Display
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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-linksetup.html
Contact [email protected] for setup
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