Transcript genome-browser

Genome Browser
Tomer Altman
Bioinformatics Research Group
SRI, International
August 19th, 2009
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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 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 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
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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
displayed
 Add External Track


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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 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
 Can
be stored as DBLINKS on gene frames
 http://bioinformatics.ai.sri.com/ptools/ortholog-linksetup.html
when many PGDBs: grows as N2
 Ortholog-Link MySQL DB is used for BioCyc WWW site
 Contact [email protected] for setup
 Problem
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