sri international bioinformatics 1 genome browser tomer altman bioinformatics research group sri,...
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SRI International Bioinformatics1
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 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