browsing the genome
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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 GFFGFFchr5 EST exon 92719127 92719406 . + 0 BEchr5 EST exon 92719127 92719406 . + 0 BEchr5 EST exon 92731587 92731784 . + 0 BEchr5 EST exon 92731587 92731784 . + 0 BE
BedBedchr5 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