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Browsing the Genome

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

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  1. Browsing the Genome Using Genome Browsers to Visualize and Mine Data

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. UCSC Outline • Navigating • Configuring Browser • Extracting data

  8. Home Page

  9. BLAT

  10. BLAT Results

  11. Standard Query

  12. Query Results

  13. Graphical Interface

  14. Configuring Display

  15. Components

  16. Get DNA

  17. Configuring DNA

  18. DNA STS Highlighted

  19. Tracks

  20. Track Display

  21. Human SDAD1

  22. Convert

  23. Mouse Sdad1

  24. EST Track

  25. Entry Data

  26. Viewing Exons

  27. Integrate Specific Data

  28. 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)

  29. Add Custom Tracks

  30. 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 -

  31. Display of Custom Tracks

  32. Configure Track Display

  33. Save PDF

  34. Table Browser

  35. Sample Table Data

  36. Proteome Browser

  37. Protein Sequence

  38. Protein Characteristics

  39. Structure Information

  40. Summary of UCSC • Different ways of querying genome • Control over graphical display • Vast amount of genomic data • Ability to collect that data

  41. However • UCSC does not include my genome • Actually no genome browser supports my genome

  42. 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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