copyright openhelix. no use or reproduction without express written consent 2 overview of genome...

Copyright OpenHelix. No use or reproduction without express written

consent 2

Overview of Genome Browsers

Materials prepared byWarren C. Lathe, Ph.D. Mary Mangan, Ph.D.Jennifer Williams, Ph.D.www.openhelix.com

Copyright OpenHelix. No use or reproduction without express written consent 3

Genome Browsers Agenda

Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary

Ensembl Genome Browser: http://www.ensembl.orgUCSC Genome Browser: http://genome.ucsc.eduNCBI Map Viewer: http://ncbi.nlm.nih.gov/mapview

IMG: http://img.jgi.doe.govGBrowse: http://gmod.org/wiki/Gbrowse


Exponential Growth in Genomic Sequence Data

Data from www.genomesonline.org &

http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj

# of genomesNearly

3,000+ completedgenomes

Official “15 year” Human Genome Project:

1990-2003

First 2 bacterial genomes complete

First eukaryotecomplete

(yeast) First metazoancomplete(flatworm)


2000: 230 databases and tools listed in compilation1996: first annual

compilation of databases and tools lists 57 databases and tools

The annual database

issue of Nucleic Acids

Research has grown

exponentially 2006: 856 databases and tools listed in compilation

A Concurrent Explosion in Databases & Tools

2011: 1330 databases and tools

http://nar.oxfordjournals.org/content/vol38/suppl_1/index.dtl


[Human] Genome BrowsersNot limited to

only human data

EBIEnsembl

NCBIMap Viewer UCSC Genome Browser


IMG: Integrated Microbial Genomes

IMG: http://img.jgi.doe.gov

Currently

over

6000

genomes

Not limited toonly microbial data


GBrowse: Generic Genome Browser

photo: NIH

http://gmod.org/wiki/Gbrowse


Genome Browsers Provide Context

IMG

EBIEnsembl

NCBIMap Viewer

UCSC Genome Browser

GBrowse


genes & predictions

variations & repeats

cross-speciescomparative data

& many more types of data from expression& regulation to mRNA and ESTs…

Gene X

DescriptionTranscript dataStructureGene OntologyPathway DataHomologous GenesExpression DataEtc….

Organized Data Based on Chromosome Location

tra

cks


Ensembl Homepage

www.ensembl.org

Click

or here

↔

+

BUILT, MAINTAINED, & FUNDED BY:


Ensembl: An Example

Jump to other

browsers –

UCSC & NCBI

Click for

more

details

tra

cks

tra

cks

Copyright OpenHelix. No use or reproduction without express written consent

Ensembl: Many Additional Toolsbest scoring

matchBLAST/BLAT

data retrievaland download

BioMart

Other Ensembl Installations

EnsemblMetazoa EnsemblPlants EnsemblFungi EnsemblProtists EnsemblBacteria


http://www.ensembl.org/info/about/species.html


UCSC Genome Browser Homepage

http://genome.ucsc.edu

Genome Bioinformatics Group (UCSC, University of California,

Santa Cruz)


UCSC Genome Browser

Jump to

Ensembl

& NCBIControls for top data tracks displayed are in lower page section

Groups of Tracks

Tracks

Collapse/expand groups

Groups of Tracks

Track

display

controls

tra

cks


Many Tools & Options Available

Get DNA,

Customize Output

Access to a tremendous amount

of information!

BLAT Search

UCSC Browser Other Installations

Archaeal genomes Arabidopsis Malaria HIV





Ensembl Genome Browser: http://www.ensembl.orgUCSC Genome Browser: http://genome.ucsc.edu

NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewIMG: http://img.jgi.doe.gov

GBrowse: http://gmod.org/wiki/Gbrowse


Map Viewer Homepage

http://ncbi.nlm.nih.gov/mapview

Select

a

species


NCBI Map Viewer Browser Page

Contig map

Sequence map (UniGene)

Sequence map (Genes_seq)

Default Maps – easy to change

Ideogram

Scroll

down to

Summary

of Maps

Copyright OpenHelix. No use or reproduction without express written consent 24Copyright OpenHelix. No use or reproduction without express written consent 24

Map Viewer Provides Many Tools & Options

BLAST Searches

Use Maps & Optionsto add/remove maps

AdvancedSearches

Clone Finder


IMG: Integrated Microbial Genomes

IMG: http://img.jgi.doe.gov

Many species,

but focus

is microbial


IMG Gene Report – Extensive & Detailed

DNA Sequence

Protein Sequence

Pathway Map

candidate enzyme or product name


IMG Gene Report – Evidence of Functions

orthologs

domains


IMG Gene Report: Many Tools & Links

IMG BLAST form

IMG phylogenetic search

Homology Toolkit

Use MyIMG to:Upload a set of Genomes,Set Search Preferences,

Upload Gene Annotations

MyIMG


GBrowse: Generic Genome Browser

http://gmod.org/wiki/Gbrowse

GBrowse

- developed by GMOD Generic Model Organism Database- web application to explore genomes- free software- goal: simplify & standardize MOD Model Organism Databases

http://genome.cshlp.org/content/12/10/1599.long

Popular


GBrowse: a Popular Viewer Human GenomeSegmental DuplicationDatabase

bird’s eye view...

...or zoom in for details

customize it

colored glyphs(icons)


GBrowse: Both Universal & UniqueU N I V E R S A L A P P E A R A N C E

U N I Q U E A P P E A R A N C E

Tracks

Learn GBrowse once – use it everywhere!

Customize your view


WebGBrowse & JBrowse

http://webgbrowse.cgb.indiana.edu/webgbrowse/cgi-bin/uploadData

AdditionalOptions

http://gmod.org/wiki/JBrowse


IGV: Integrative Genomics Viewer

IGV: http://www.broadinstitute.org/igv/

Datasets & Genomes available


Many Additional Genome Browsers AvailableARGO:

http://www.broadinstitute.org/annotation/argo/

IGB: http://igb.bioviz.org/

CGView: http://wishart.biology.ualberta.ca/cgview/

Gaggle: http://gaggle.systemsbiology.net/docs/geese/genomebrowser/


Genome Browsers - Similarities & Differences

IMG

EBIEnsembl

NCBIMap Viewer

UCSC Genome Browser

GBrowse


Summary of These Genome BrowsersChromosome orientation

Species totals

Oct 2011

Human

Genome

Oct 2011

Custom

track tool

Custom query tool

Sequence search

Ensembl (main site)

horizontal 58 GRCh37 DAS BioMart BLAST or

BLAT

NCBI Map

Viewer

vertical 123 NCBI build 37.1

BLAST

UCSC

Genome

Browser

horizontal 53 GRCh37 Custom

Tracks

Table

Browser

BLAT

IMG linear/

horizontal

6000+ Yes IMG Annotation Site

My IMG BLAST

GBrowse horizontal 100+ at different

sites

various DAS BLAST


Compare & Contrast of These Genome Browsers Organisms included (example of focus)

Restriction enzyme data

Search for locations by protein domain

Search for overlap in datasets

Sort genes by chosen criteria

Sequence similarity search on multiple species

Ensembl

(main site)

mostly vertebrate

Yes Yes Restricted:

BioMart

BioMart Yes

NCBI Map

Viewer

Range; plant, fungi, insects, vertebrate

No No No My NCBI

Restricted:

Selected groups

UCSC

Genome

Browser

vertebrate, insect, model organisms,

others

Yes Restricted

Table Browser

Yes:

Table Browser

Gene

Sorter

No

IMG All Microbes, 16 model eukaryotes

No Yes Phylo-

genetically

Some options

Yes

GBrowse Varies by individual implementation at different sites


GBrowse & Newer Genome Browsers

photo: NIH

Basis of somany browsers

GBrowse

Many NewerBrowsers


OpenHelix Tutorials Available for Many Browsers

More detail on software functionality Exercises and slides Free provider-sponsored materials: www.openhelix.com

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