SRI International Bioinformatics 1 Genome Browser Markus Krummenacker Bioinformatics Research Group...

SRI International Bioinformatics1

Genome Browser

Markus Krummenacker

Bioinformatics Research Group

SRI, International

Q2 2013


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 pageClick on the button by the base pair coordinates of a gene displayMenu: Chromosome --> Enter Genome Browser


From Current Organism:


From Menu:


The Genome Browser


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 mapSpecifying the start & end base-pair positionsEntering a gene nameNavigation arrows


Navigation Features


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

membership. Greenish = experimental ev.Promoters and terminators are also displayed


Chromosome Menu

Enter Genome BrowserFor PGDBs with multiple replicons

Show Sequence of a Segment of ChromosomeSub-sequence of the replicon, or its reverse-compliment

Print PosterGenerate a wall poster-sized PostScript file with the entire genome

displayedAdd External Track

Display GFF file data in context


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.


How to Display External Tracks:

Menu: Chromosome -> Enter Genome BrowserClick “Show Tracks”Menu: Chromosome -> Add External TrackEnter URL or browse local filesCan be repeated multiple times to display several data

sets


Browser with Tracks Shown


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


Genome Omics Viewer


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.


Comparative Genome Browser Display


Ortholog-Links

Ortholog-Link MySQL DB is used for BioCyc WWW site

Get-Orthologs-From-SRI parameter in ptools-init.dathttp://bioinformatics.ai.sri.com/ptools/ortholog-link-

setup.htmlContact [email protected] for setup

SRI International Bioinformatics 1 Genome Browser Markus Krummenacker Bioinformatics Research Group...

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