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Version14c_0908 Copyright OpenHelix. No use or reproduction without express written consent 3 The UCSC Genome Browser Additional Tools Materials prepared by Warren C. Lathe III, Ph.D. Mary Mangan, Ph.D. Updated: Q3 2008
Copyright OpenHelix. No use or reproduction without express written consent4 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises Introduction
Copyright OpenHelix. No use or reproduction without express written consent5 The UCSC Homepage:
Copyright OpenHelix. No use or reproduction without express written consent6 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises
Copyright OpenHelix. No use or reproduction without express written consent77 Gene Sorter From homepage select “Gene Sorter”
Copyright OpenHelix. No use or reproduction without xpress written consent88 Gene Sorter Example Sort genes by similarity criteria
Copyright OpenHelix. No use or reproduction without express written consent99 Choose Genome Choose Assembly Type in gene name or accession number Gene Sorter: Chose Genome and Gene
Copyright OpenHelix. No use or reproduction without express written consent10 Gene Sorter: Similarity Sorting Options Choose from several similarity sorting options, varies by assembly & species
Copyright OpenHelix. No use or reproduction without express written consent11 Gene Sorter: Configure Configure Choose columns of data to display Choose order of display columns Some columns can be configured
Copyright OpenHelix. No use or reproduction without express written consent12 Gene Sorter: Saving Configuration Configure Hide, show all columns or return to default Save configurations and load previous
Copyright OpenHelix. No use or reproduction without express written consent13 Gene Sorter: Adding Custom Data Configure Custom columns of user’s data Custom data
Copyright OpenHelix. No use or reproduction without express written consent14 Gene Sorter: Filters Filter Filter data of columns displayed or those not displayed List genes List all genes found with selected filters
Copyright OpenHelix. No use or reproduction without express written consent15 Gene Sorter: Save Filters Save filter trim_name Click save
Copyright OpenHelix. No use or reproduction without express written consent16 Gene Sorter: Load Filters Saved filtersChoose filter & load
Copyright OpenHelix. No use or reproduction without express written consent17 Gene Sorter: Submit Filters Submit
Copyright OpenHelix. No use or reproduction without express written consent18 Gene Sorter: Get Results Go to results
Copyright OpenHelix. No use or reproduction without express written consent19 Gene Sorter: Sort Results by Name Re-sort Re-sort genes based on gene clicked using same parameters. Description
Copyright OpenHelix. No use or reproduction without express written consent20 Gene Sorter: VisiGene Results VisiGene Open UCSC VisiGene image page for gene.
Copyright OpenHelix. No use or reproduction without express written consent21 Gene Sorter: Alignment Results Alignment Amino acid alignment between reference gene and gene protein products
Copyright OpenHelix. No use or reproduction without express written consent22 Gene Sorter: Open Genome Browser Browser Open Genome Browser to location of chosen gene
Copyright OpenHelix. No use or reproduction without express written consent23 Gene Sorter: Open Details Page Description Open gene details page of chosen gene
Copyright OpenHelix. No use or reproduction without express written consent24 Gene Sorter: Gene Sequences Sequences Get sequences Choose sequence type, obtain FASTA file of all gene sequences
Copyright OpenHelix. No use or reproduction without express written consent25 Gene Sorter: Text File of Data Data text Obtain tab-delineated file of all displayed gene data
Copyright OpenHelix. No use or reproduction without express written consent26 Gene Sorter Sort genes by similarity criteria
Copyright OpenHelix. No use or reproduction without express written consent27 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises
Copyright OpenHelix. No use or reproduction without express written consent28 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)
Copyright OpenHelix. No use or reproduction without express written consent29 In-Silico PCR Results Genomic location shown, links to Genome Viewer locationyour primers Your primers displayed, flipped if necessary Predicted genomic sequence shown Tm for primers Primer melting temperatures provided size Product size shown
Copyright OpenHelix. No use or reproduction without express written consent30 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises
Copyright OpenHelix. No use or reproduction without express written consent31 VisiGene Image Browser VisiGene: Biological image data Expression in cells and tissues; mRNA or protein Search by symbol, author, body parts, IDs, stages…
Copyright OpenHelix. No use or reproduction without express written consent32 VisiGene Results List of results Select one to view Links and details
Copyright OpenHelix. No use or reproduction without express written consent33 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises
Copyright OpenHelix. No use or reproduction without express written consent34 Proteome Browser Collection of protein level data Access from homepage or UCSC Gene pages
Copyright OpenHelix. No use or reproduction without express written consent35 Proteome Browser Results Protein level data Exons illustrated, link to browser Domains, family Structure Pathways
Copyright OpenHelix. No use or reproduction without express written consent36 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises
Copyright OpenHelix. No use or reproduction without express written consent37 Other Features Utilities: other small useful tools liftOver: to migrate between genome versions Dusters: to clean up stray characters in sequence files Tree Maker
Copyright OpenHelix. No use or reproduction without express written consent38 Explore! genomewiki.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent39 UCSC Genome Browser Agenda UCSC Genome Browser: Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises
Copyright OpenHelix. No use or reproduction without express written consent40 Hands-on session for UCSC Additional Tools 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
Copyright OpenHelix. No use or reproduction without express written consent41 Notice: The materials and slides offered are for non-commercial use only. Reproduction, distribution and/or use for commercial purposes is strictly prohibited. Copyright 2008, OpenHelix, LLC