Browsing the Genome Using Genome Browsers to Visualize and Mine Data

Browsing the GenomeBrowsing the Genome

Using Genome Browsers to Using Genome Browsers to Visualize and Mine DataVisualize and Mine Data

Genome BrowsersGenome Browsers

Software designed to enable a user Software designed to enable a user to access and display sequence data to access and display sequence data

Provide a visual correlation for Provide a visual correlation for different types of informationdifferent types of information

Organize large amounts of genome Organize large amounts of genome sequence datasequence data

Several Different Genome Several Different Genome BrowsersBrowsers

Common features:Common features: Coordinate system is based on the buildCoordinate system is based on the build Zoom in and outZoom in and out Gene features aligned to genomeGene features aligned to genome

Major Differences:Major Differences: Each Browser has a very different look and feelEach Browser has a very different look and feel Navigating through the informationNavigating through the information

Main Genome Browser Main Genome Browser RepositoriesRepositories

EnsemblEnsembl NCBI (Entrez) - BLASTNCBI (Entrez) - BLAST UCSC - BLATUCSC - BLAT

Ensembl, NCBI, and UCSC use the Ensembl, NCBI, and UCSC use the same human genome assembly that same human genome assembly that is generated by NCBI but release is generated by NCBI but release timing is different between sitestiming is different between sites

UCSCUCSC

Vertebrates, Deuterostomes, Insects, Vertebrates, Deuterostomes, Insects, Nematodes, YeastNematodes, Yeast

Entry into genome sequence via BLATEntry into genome sequence via BLAT Table BrowserTable Browser Creation of PDFCreation of PDF Provides access to all the data produced by Provides access to all the data produced by

the project, and to the software used to the project, and to the software used to analyze and present itanalyze and present it

Site produces and maintains annotation Site produces and maintains annotation trackstracks

Aligned Annotation TracksAligned Annotation Tracks

Genomic data: known genes, predicted Genomic data: known genes, predicted genes, ESTs, mRNAs, CpG islands, genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal assembly gaps and coverage, chromosomal bands, mouse homologies, and morebands, mouse homologies, and more

Annotation tracks are both computed at Annotation tracks are both computed at UCSC from publicly available sequence data UCSC from publicly available sequence data and provided by collaboratorsand provided by collaborators

Users can also add their own custom tracks Users can also add their own custom tracks to the browser to the browser

UCSC OutlineUCSC Outline

NavigatingNavigating Configuring BrowserConfiguring Browser Extracting dataExtracting data

Home PageHome Page

BLATBLAT

BLAT ResultsBLAT Results

Standard QueryStandard Query

Query ResultsQuery Results

Graphical InterfaceGraphical Interface

Configuring DisplayConfiguring Display

ComponentsComponents

Get DNAGet DNA

Configuring DNAConfiguring DNA

DNA STS HighlightedDNA STS Highlighted

TracksTracks

Track DisplayTrack Display

Human SDAD1Human SDAD1

ConvertConvert

Mouse Sdad1Mouse Sdad1

EST TrackEST Track

Entry DataEntry Data

Viewing ExonsViewing Exons

Integrate Specific DataIntegrate Specific Data

Custom TracksCustom Tracks

User provided annotation data User provided annotation data Can be in standard GFF format or in a Can be in standard GFF format or in a

format designed specifically for UCSC format designed specifically for UCSC Genome Browser, including GTF, PSL, Genome Browser, including GTF, PSL, BED, WIG, and microarray (BED15) BED, WIG, and microarray (BED15)

Add Custom TracksAdd Custom Tracks

Sample Custom TracksSample Custom Tracks

GFFGFF

chr5 EST exon 92719127 92719406 . + 0 BEchr5 EST exon 92719127 92719406 . + 0 BE

chr5 EST exon 92731587 92731784 . + 0 BEchr5 EST exon 92731587 92731784 . + 0 BE

BedBed

chr5 92715320 92715326 miR-194 1 -chr5 92715320 92715326 miR-194 1 -

chr5 92715467 92715474 miR-124.1 3 -chr5 92715467 92715474 miR-124.1 3 -

chr5 92715467 92715473 miR-124/506 1 -chr5 92715467 92715473 miR-124/506 1 -

Display of Custom TracksDisplay of Custom Tracks

Configure Track DisplayConfigure Track Display

Save PDFSave PDF

Table BrowserTable Browser

Sample Table DataSample Table Data

Proteome BrowserProteome Browser

Protein SequenceProtein Sequence

Protein CharacteristicsProtein Characteristics

Structure InformationStructure Information

Summary of UCSCSummary of UCSC

Different ways of querying genomeDifferent ways of querying genome Control over graphical displayControl over graphical display Vast amount of genomic dataVast amount of genomic data Ability to collect that dataAbility to collect that data

HoweverHowever

UCSC does not include my genomeUCSC does not include my genome

Actually no genome browser Actually no genome browser supports my genomesupports my genome

Custom Browser SoftwareCustom Browser Software

GBrowse is a combination of GBrowse is a combination of database and interactive Web page database and interactive Web page for manipulating and displaying for manipulating and displaying annotations on genomes annotations on genomes

Annotation Browsers- Argo and Annotation Browsers- Argo and ApolloApollo