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The Genome

The Genome. Genome Browser Training. Part 1. Materials developed by: Warren C. Lathe, Ph.D. and Mary Mangan, Ph.D. info@openhelix.com. Organization of genomic data…. chromosome band. sts sites. gap locations. known genes. Annotation Tracks. predicted genes. microarray/expression data.

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The Genome

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  1. The Genome Genome Browser Training Part 1 Materials developed by: Warren C. Lathe, Ph.D. and Mary Mangan, Ph.D. info@openhelix.com

  2. 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

  3. A sample of what we will find:

  4. Agenda • Basic searches using the Genome Browser • Text searching, Sequence Searching (BLAT) • In Silico PCR, Proteome Browser • Hands-on session for Basic Searches • Gene Sorting search using the Gene Sorter • Advanced searching using the Table Browser • Custom Tracks • Hands-on session for Sorter, Table Browser, and Custom Tracks

  5. The UCSC Home page: genome.ucsc.edu navigate navigate General information Specific information— new features, current status, etc.

  6. The Genome Browser Gatewaystart page, basic search Helpful search examples, suggestions below text/ID searches • 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

  7. The Genome Browser Gatewaystart page choices, February 2005 1 2 3 6 5 4 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

  8. The Genome Browser Gatewaysample search for Human BRCA1 select • Often you will have to select the • right gene from a results list • Sometimes, you will go directly • to a browser image (use an ID) • AF005068, breast cancer 1, early onset • Sample search: human, May 2004 assembly, BRCA1

  9. Overview of the wholeGenome Browser page(first day, new human release) } Genome viewer section Track and image controls (day 1 = 40 tracks)

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

  11. Different species, different tracks, same software

  12. Sample Genome Viewer image, BRCA1 region Genome backbone STS markers Known genes RefSeq genes CCDS Gene predictions GenBank mRNAs GenBank ESTs conservation SNPs repeats

  13. Visual Cues on the Genome Browser 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 For some tracks, the height of a bar is increased likelihood of an evolutionary relationship

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

  15. Annotation Track display options enforce changes Change track view Links to details 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 • Some data is ON or OFF by default

  16. Annotation Track options, defined • 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 • Hide: removes a track from view

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

  18. Annotation Track options, if altered….important point: the browser remembers! To clear your “cart” or parameters, click default tracks OR • Session information (the position you were examining) • Track choices (squish, pack, full, etc) • Filter parameters (if you changed the colors of any items, or the subset to be displayed) …are all saved on your computer. When you come back in a couple of days to use it again, these will still be set. You may—or may not—intend this.

  19. Clicking an annotation line, new page of detailed information Click the line New web page opens Many details and links to more data about BRCA1 You will get detail for that single item you click Example: click on the BRCA1 Black “Known Genes” line

  20. Click annotation track = BRCA1 “Known gene” detail page SNP detail page sample informative description Not all genes have This much detail. Different annotation tracks carry different detail data. other resource links links to sequences microarray data mRNA secondary structure protein domains/structure homologs in other species Gene Ontology™ descriptions mRNA descriptions pathways

  21. Getting the sequencesGet DNA, with Extended Options; or Details pages • Use the DNA link at the top • Plain or Extended options • Change colors, fonts, etc.

  22. Getting the sequencesAnother way: from details pages Click the line • Genomic • (many options) • mRNA • Protein Click a track, go to Sequence section of details page

  23. Agenda • Basic searches using the Genome Browser • Text searching,Sequence Searching (BLAT) • In Silico PCR, Proteome Browser • Hands-on session for Basic Searches • Gene Sorting search using the Gene Sorter • Advanced searching using the Table Browser • Custom Tracks • Hands-on session for Sorter, Table Browser, and Custom Tracks

  24. Accessing the BLAT tool • Rapid searches by INDEXING the entire genome • Works best with high similarity matches • See documentation and publication for details BLAT = BLAST-like Alignment Tool

  25. BLAT tool overview: www.openhelix.com/sampleseqs.html • Make choices • Paste one or more sequences DNA limit 25000 bases Protein limit 10000 aa 25 total sequences • Or upload Submit

  26. BLAT results, with links sorting • 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)

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

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

  29. Agenda • Basic searches using the Genome Browser • Text searching,Sequence Searching (BLAT) • In Silico PCR, Proteome Browser • Hands-on session for Basic Searches • Gene Sorting search using the Gene Sorter • Advanced searching using the Table Browser • Custom Tracks • Hands-on session for Sorter, Table Browser, and Custom Tracks

  30. In Silico PCR: find genomic sequence using primers • Select genome • Enter primers • Minimum 15 bases • Flip reverse primer? • Submit (note: the tool does not handle ambiguous bases at this time—don’t use Ns)

  31. In Silico PCR: results Tm for primers location size your primers • Your primers displayed, flipped if necessary • Product size shown • Primer melting temperatures provided • Genomic location shown, links to Genome Viewer • Predicted genomic sequence shown

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

  33. Agenda • Basic searches using the Genome Browser • Text searching,Sequence Searching (BLAT) • In Silico PCR, Proteome Browser • Hands-on session for Basic Searches • Gene Sorting search using the Gene Sorter • Advanced searching using the Table Browser • Custom Tracks • Hands-on session for Sorter, Table Browser, and Custom Tracks

  34. Hands-on session for basic searches • Exercises on the handouts • We will walk through them together • 2 styles: questions only, and step-by-step • When we are finished the formal exercises, we can help you to investigate issues that you want to understand for your research

  35. UCSC Genome Browser credits • http://genome.ucsc.edu/goldenPath/credits.html • Funding, data sources, external contributors Development team: http://genome.ucsc.edu/staff.html • Led by David Haussler and Jim Kent • Dozens of staff and students also work to bring you this software and data

  36. Agenda • Basic searches using the Genome Browser • Text searching, Sequence Searching (BLAT) • In Silico PCR, Proteome Browser

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