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Genome Browser

Tomer AltmanBioinformatics Research Group

SRI, InternationalJanuary 28th, 2008

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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 fulllength, lowresolution 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 pseudogenes are crossed outGenes wrapping around line have 'zigzag'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-

complimentPrint 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.

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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