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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.
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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, mRNAs, CpG 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
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 (BED15)
Sample Custom Tracks • GFF chr5 EST exon 92719127 92719406 . + 0 BE chr5 EST exon 92731587 92731784 . + 0 BE • Bed chr5 92715320 92715326 miR-194 1 - chr5 92715467 92715474 miR-124.1 3 - chr5 92715467 92715473 miR-124/506 1 -
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