Browsing the Genome Using Genome Browsers to Visualize and Mine Data
Genome Browsers Software designed to enable a user to access and display sequence data Provide a visual correlation for different types of information Organize large amounts of genome sequence data
Several Different Genome Browsers Common features: Coordinate system is based on the build Zoom in and out Gene features aligned to genome Major Differences: Each Browser has a very different look and feel Navigating through the information
Main Genome Browser Repositories Ensembl NCBI (Entrez) - BLAST UCSC - BLAT Ensembl, NCBI, and UCSC use the same human genome assembly that is generated by NCBI but release timing is different between sites
UCSC Vertebrates, Deuterostomes, Insects, Nematodes, Yeast Entry into genome sequence via BLAT Table Browser Creation of PDF Provides access to all the data produced by the project, and to the software used to analyze and present it Site produces and maintains annotation tracks
Aligned Annotation Tracks Genomic data: known genes, predicted genes, ESTs, m. RNAs, Cp. G islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more Annotation tracks are both computed at UCSC from publicly available sequence data and provided by collaborators Users can also add their own custom tracks to the browser
UCSC Outline Navigating Configuring Browser Extracting data
Home Page
BLAT
BLAT Results
Standard Query
Query Results
Graphical Interface
Configuring Display
Components
Get DNA
Configuring DNA
DNA STS Highlighted
Tracks
Track Display
Human SDAD 1
Convert
Mouse Sdad 1
EST Track
Entry Data
Viewing Exons
Integrate Specific Data
Custom Tracks User provided annotation data Can be in standard GFF format or in a format designed specifically for UCSC Genome Browser, including GTF, PSL, BED, WIG, and microarray (BED 15)
Add Custom Tracks
Sample Custom Tracks GFF chr 5 EST exon 92719127 92719406. + 0 BE chr 5 EST exon 92731587 92731784. + 0 BE Bed chr 5 92715320 92715326 mi. R-194 1 chr 5 92715467 92715474 mi. R-124. 1 3 chr 5 92715467 92715473 mi. R-124/506 1
Display of Custom Tracks
Configure Track Display
Save PDF
Table Browser
Sample Table Data
Proteome Browser
Protein Sequence
Protein Characteristics
Structure Information
Summary of UCSC Different ways of querying genome Control over graphical display Vast amount of genomic data Ability to collect that data
However UCSC does not include my genome Actually no genome browser supports my genome
Custom Browser Software GBrowse is a combination of database and interactive Web page for manipulating and displaying annotations on genomes Annotation Browsers- Argo and Apollo
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Browsing_the_Genome.ppt