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UCSC Genome Browser

UCSC Genome Browser. The Progress. Today - 85,759,586,764. Official “15 year” Human Genome Project: 1990-2003. Data from NCBI and TIGR ( www.ncbi.nlm.nih.gov and www.tigr.org ). Database and Tool Explosion. 2000 : 230 databases and tools listed in compilation.

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UCSC Genome Browser

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  1. UCSC Genome Browser

  2. The Progress Today - 85,759,586,764 Official “15 year” Human Genome Project: 1990-2003 Data from NCBI and TIGR (www.ncbi.nlm.nih.gov and www.tigr.org )

  3. Database and Tool Explosion 2000: 230 databases and tools listed in compilation 1996: first annual compilation of databases and tools lists 57 databases and tools 2008: 1078 databases and tools listed in compilation The annual database issue of Nucleic Acids Research has grown exponentially

  4. Genome Browsers UCSC Genome Browser EBI Ensembl NCBI Map Viewer

  5. Organizing the Genome genes & predictions variations and repeats cross-species comparative data Gene X Description Transcript data Structure Gene Ontology Pathway Data Homologous Genes Expression Data Etc…. and many more types of data from expression and regulation to mRNA and ESTs…

  6. UCSC Genome Browser: genome.ucsc.edu

  7. UCSC Genome Browser

  8. Organization of genomic data… chromosome band sts sites gap locations known genes Annotation Tracks predicted genes microarray/expression data evolutionary conservation SNPs repeated regions more… sequence Genome backbone: base position number Links out to more data

  9. gene details comparisons Annotation Tracks SNPs A sample of what we will find: official sequence

  10. text/ID searches Helpful search examples, suggestions below The Genome Browser Gatewaystart page, basic search • Use this Gateway to search by: • Gene names, symbols • Chromosome number: chr7, or region: chr11:1038475-1075482 • Keywords: kinase, receptor • IDs: NP, NM, OMIM, and more… • See lower part of page for help with format

  11. 3 2 1 6 The Genome Browser Gatewaystart page choices, December 2006 4 5 Make your Gateway choices: • Select Clade • Select species: search 1 species at a time • Assembly: the official backbone DNA sequence • Position: location in the genome to examine • Image width: how many pixels in display window; 5000 max • Configure: make fonts bigger + other choices

  12. select The Genome Browser Gatewaysample search for Human TP53 • Sample search: human, March 2006 assembly, tp53 • Select from results list • ID search may go right to a viewer page, if unique

  13. Mapping and Sequencing Tracks Genes and Gene Prediction Tracks mRNA and EST Tracks Expression and Regulation Comparative Genomics Variation and Repeats Overview of the wholeGenome Browser page } Genome viewer section Groups of data

  14. STS markers Known genes RefSeq genes GenBank seqs 17 species compared single species compared SNPs repeats Sample Genome Viewer image, TP53 region base position

  15. Tick marks; a single location (STS, SNP) < < < < < < < exon exon < exon ex 3' UTR 5' UTR Intron, and direction of transcription <<< or >>> Track colors may have meaning—for example, Known Gene track: • If there is a corresponding PDB entry, = black • If there is a corresponding NCBI Reviewed seq, = dark blue • If there is a corresponding NCBI Provisional seq, = light blue Visual Cues on the Genome Browser For some tracks, the height of a bar is increased likelihood of an evolutionary relationship (conservation track)

  16. Options for Changing Images: Upper Section Walk left or right Zoom in Zoom out • Change your view or location with controls at the top • Use “base” to get right down to the nucleotides • Configure: to change font, window size, more… Specify a position fonts, window, more click to zoom 3x and re-center

  17. Change track view Annotation Track display options • Some data is ON or OFF by default enforce changes Links to info and/or filters • Menu links to info about the tracks: content, methods • You change the view with pulldown menus • After making changes, REFRESH to enforce the change

  18. Dense: all items collapsed into a single line • Squish: each item = separate line, but 50% height + packed • Pack: each item separate, but efficiently stacked (full height) • Full: each item on separate line Annotation Track options, defined • Hide: removes a track from view

  19. enforce any changes (hide, full, squish…) reset, back to defaults start from scratch Reset, Hide, Configure or Refresh to change settings • You control the views • Use pulldown menus • Configure options page

  20. Click the item New web page opens Many details and links to more data about TP53 Click Any Viewer Object for Details Example: click your mouse anywhere on the TP53 line

  21. informative description other resource links links to sequences microarray data mRNA secondary structure protein domains/structure homologs in other species Gene Ontology™ descriptions mRNA descriptions pathways Click annotation track item for details pages Not all genes have This much detail. Different annotation tracks carry different data.

  22. Get DNA, with Extended Case/Color Options • Use the DNA link at the top • Plain or Extended options • Change colors, fonts, etc.

  23. Click the line Click the item sequence section on detail page Get Sequence from Details Pages Click a track, go to Sequence section of details page

  24. Accessing the BLAT tool • Rapid searches by INDEXING the entire genome • Works best with high similarity matches • See documentation and publication for details • Kent, WJ. Genome Res. 2002. 12:656 BLAT = BLAST-like Alignment Tool

  25. Make choices • Paste one or more sequences DNA limit 25000 bases Protein limit 10000 aa 25 total sequences • Or upload BLAT tool overview: submit

  26. BLAT results, with links • Results with demo sequences, settings default; sort = Query, Score • Score is a count of matches—higher number, better match • Click browser to go to Genome Browser image location (next slide) • Click details to see the alignment to genomic sequence (2nd slide) go to browser/viewer go to alignment detail sorting

  27. click to flip frame query • Watch out for reading frame! Click - - - > to flip frame • Base position = full and zoomed in enough to see amino acids BLAT results, browser link • From browser click in BLAT results • A new line with your Sequence from BLAT Search appears!

  28. Your query Genomic match, color cues Side-by-side alignment yours genomic BLAT results,alignment details

  29. Proteome Browser • Access from homepage or Known Gene pages • Exon diagram, amino acids… • Many protein properties (pI, mw, composition, 3D…) more data

  30. In-Silico PCR: Find genomic sequence using primers • Select genome • Enter primers • Minimum 15 bases • Flip reverse primer? • Submit

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