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Copyright OpenHelix. No use or reproduction without express written consent 1 Important note to slide users: PC users Mac users To maintain the color schemes/cues and the animations, if you import these slides into other slide sets please click the checkbox in the PowerPoint Insert window that maintains slide format. Otherwise important information may be lost. Copyright OpenHelix. No use or reproduction without express written consent 2 The UCSC Genome Browser Introduction Materials prepared by Mary Mangan, Ph.D. www.openhelix.com Version 21a_1012 Copyright OpenHelix. No use or reproduction without express written consent 3 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 4 Organization of Genomic Data Annotation Tracks sequence Reference genome: base position number chromosome band gap locations known genes predicted genes phenotype and disease Links out to more data enhancer/promoter data microarray/expression data evolutionary conservation SNPs and structural variation repeated regions more… Copyright OpenHelix. No use or reproduction without express written consent 5 A Sample of the UCSC Genome Browser gene details reference sequence Annotation Tracks comparisons SNPs Copyright OpenHelix. No use or reproduction without express written consent 6 UCSC Genome Browser Credits Development team: http://genome.ucsc.edu/staff.html Led by David Haussler and Jim Kent Dozens of staff and students bring you this software and data http://genome.ucsc.edu/goldenPath/credits.html Funding, data sources, external contributors Copyright OpenHelix. No use or reproduction without express written consent 7 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 8 The UCSC Homepage: http://genome.ucsc.edu navigate navigate General information Specific information— new features, current status, etc. Copyright OpenHelix. No use or reproduction without express written consent 9 Gateway: Start Page for a Basic Search text/ID searches Use this Gateway to search: Gene names, symbols, IDs Chromosome number: chr7, or region: chr11:1038475-1075482 Keywords: kinase, receptor See lower part of page for help with format Copyright OpenHelix. No use or reproduction without express written consent 10 UCSC Genome Browser Gateway 1 2 3 4 5 assembly Make your Gateway choices: 1. Select clade + genome = species: search 1 species at a time 2. Assembly: the official reference DNA sequence 3. Position: location in the genome to examine, or text search 4. Track search to find data types of interest (annotation tracks) 5. Configure: make fonts bigger + other display choices Copyright OpenHelix. No use or reproduction without express written consent 11 Sample Search for Human TP53 select Sample search: human, February 2009 assembly, tp53 uc002gij.2 Select from results list; or goes to a viewer page, if unique Copyright OpenHelix. No use or reproduction without express written consent 12 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 13 } Overview of the Whole Genome Browser Page Genome viewer (2009 Human Assembly) Groups of data (Tracks) Mapping and Sequencing Tracks Phenotype and Disease Tracks Genes and Gene Prediction Tracks (including sno/miRNA data) Track data may be updated mRNA and EST Tracks Expression (such as microarray) Regulation (including TFBS) Comparative Genomics •As a group •Individual species Variation and Repeats Default settings; tracks can now be dragged in viewer (including SNPs, copy number variation) Copyright OpenHelix. No use or reproduction without express written consent 14 Different Assemblies, Species, Tracks Assemblies, Species may have different data tracks Layout, software, functions the same Copyright OpenHelix. No use or reproduction without express written consent 15 Sample Genome Viewer Image, TP53 Region scale base position UCSC genes RefSeq mRNAs & ESTs ENCODE many species compared single species compared SNPs Copyright OpenHelix. No use or reproduction without express written consent repeats 16 Visual Cues on the Genome Browser Tick marks; a single location (STS, SNP) 3' UTR exon <<< exon < exon < < < <ex 5' UTR Intron and direction of transcription <<< or >>> Track colors may have meaning—for example, UCSC Gene track: •If there is a corresponding PDB entry = black •If there is a corresponding reviewed/validated seq = dark blue •If there is a non-RefSeq seq = lightest blue Mammal cons. height of a blue bar is increased likelihood of conservation, red indicates a likelihood of faster-evolving regions Alignment indications (Conservation pairs: “chain” or “net” style) •Alignments = boxes, Gaps = lines Copyright OpenHelix. No use or reproduction without express written consent 17 Options for Changing Images: Upper Section walk zoom Tweak position or do new search Rightclick items Hold/drag mouse Drag (like Google Maps) to view section Change your view or location with controls at the top Use “base” to get right down to the nucleotides Drag tracks up and down the viewer to re-arrange Various select and focus options by clicking/dragging mouse Copyright OpenHelix. No use or reproduction without express written consent 18 Annotation Track Display Options Links to info and/or filters and color key Enforce menu changes Some data is ON or OFF by default Menu links to info about the tracks: content, methods Change track view You change the view with pulldown menus After making changes, REFRESH to enforce the change Copyright OpenHelix. No use or reproduction without express written consent 19 Basic Annotation Track Menus Defined Hide: removes a track from view 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 (may need to zoom to fit) Copyright OpenHelix. No use or reproduction without express written consent 20 Tracks with Additional Options: Filters, more…. off on Supertrack Some tracks have filters (ESTs shown; SNPs other good example) Some tracks may have undisplayed data (Yale TFBS; 2006) Super-tracks may have multiple components, various settings Copyright OpenHelix. No use or reproduction without express written consent 21 Mid-page Options to Change Settings Search for data types Flip display to Genomic 5’3’ Resets, back to defaults Fit to browser window size Start from scratch Search for data types Reset to defaults Configure options page You control the views with numerous features Copyright OpenHelix. No use or reproduction without express written consent 22 Cookies and Sessions Your browser remembers where you were (cookies) OR To clear your “cart” or parameters, click default tracks or reset Save your setup as “Session” and store/share them Requires login Lifespan: 4 months Copyright OpenHelix. No use or reproduction without express written consent 23 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 24 Click Any Viewer Object for More Details Click the item New description web page opens Many details and links to more data about TP53 Example: click your mouse anywhere on the TP53 line Copyright OpenHelix. No use or reproduction without express written consent 25 informative description other resource links links to sequences Click Annotation Track Item for Description Pages genetic association studies comparative toxicology microarray data Not all genes have this much detail. Different annotation tracks carry different data. mRNA secondary structure protein domains/structure orthologs in other species Gene Ontology™ descriptions Click a SNP to get SNP details mRNA descriptions pathways synonyms gene model Copyright OpenHelix. No use or reproduction without express written consent 26 Get DNA, with Extended Case/Color Options Get DNA 255 255 Use the View DNA link at the top Plain or Extended options Change colors, fonts, underline, etc. Copyright OpenHelix. No use or reproduction without express written consent 27 Get Sequence from Description Pages Click the item sequence section on detail page Copy whole mRNA for next segment Click an item, go to Sequence section of description page Copyright OpenHelix. No use or reproduction without express written consent 28 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 29 Accessing the BLAT Tool BLAT = BLAST-like Alignment 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 and “Help” Copyright OpenHelix. No use or reproduction without express written consent 30 BLAT Tool Interface Make choices Paste one or more sequences FASTA for more than one DNA limit 25000 bases Protein limit 10000 aa 25 total sequences submit Or upload Short seqs Copyright OpenHelix. No use or reproduction without express written consent 31 sorting Results with demo sequences, settings default; sort = Query, Score go to alignment detail go to browser/viewer BLAT Results with Hyperlinks 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) Copyright OpenHelix. No use or reproduction without express written consent 32 BLAT Results: Browser Link query From browser click in BLAT results A new track line with Your Sequence from BLAT Search appears Also a new menu to adjust Copyright OpenHelix. No use or reproduction without express written consent 33 BLAT Results, Alignment Details Your query Side by Side Alignment Genomic match, with color cues yours genomic Copyright OpenHelix. No use or reproduction without express written consent 34 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 35 Introduction Summary UCSC Genome Browser Visual cues and genomic context Many ways to alter your views Access to deeper data details Access and use sequence data Copyright OpenHelix. No use or reproduction without express written consent 36 UCSC Genome Browser Agenda Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) Summary Exercises UCSC Genome Browser: http://genome.ucsc.edu Copyright OpenHelix. No use or reproduction without express written consent 37 Hands-on Session for Introduction Exercises provided as document 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 Copyright OpenHelix. No use or reproduction without express written consent 38 Notice: The materials and slides offered are for non-commercial use only. Reproduction, distribution and/or use for commercial purposes is strictly prohibited. Copyright 2012, OpenHelix, LLC http://www.openhelix.com/ucsc Copyright OpenHelix. No use or reproduction without express written consent 39
