Copyright OpenHelix. No use or reproduction without express written consent1
GBrowse Generic Genome Browser 1.x Series Materials prepared by: Mary E. Mangan, Ph.D. Updated: Q Version 2.0
Copyright OpenHelix. No use or reproduction without express written consent3 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent4 GBrowse Introduction GBrowse developed by GMOD Generic Model Organism Database generic Genome Browser web application to explore genomes free software goal: simplify & standardize MODs Model Organism Databases
Copyright OpenHelix. No use or reproduction without express written consent5 Browsing a Genome bird’s eye view......or zoom in for details colored glyphs (icons) customize it
Copyright OpenHelix. No use or reproduction without express written consent6 GBrowse as a Standard Human Genome Segmental Duplication Database
Copyright OpenHelix. No use or reproduction without express written consent7 Citation, Documentation, Mailing List PMID:
Copyright OpenHelix. No use or reproduction without express written consent8 Administrator and Developer Resources
Copyright OpenHelix. No use or reproduction without express written consent9 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent10 Universal GBrowse Layout Human Genome Segmental Duplication Database
Copyright OpenHelix. No use or reproduction without express written consent11 Mouse GBrowse banner instructions search description details tracks cookies overview region displayedinstructions search overview details
Copyright OpenHelix. No use or reproduction without express written consent12 Opening and Closing Sections Open ViewHidden View toggle (open) (hide) control sections you want to view
Copyright OpenHelix. No use or reproduction without express written consent13 Instructions what’s allowable for searches bookmark current view and settings for re-visits to page view Detail image in SVG format restore standard settings
Copyright OpenHelix. No use or reproduction without express written consent14 Search Gene symbols Gene IDs Sequence IDs Genetic markers Relative nucleotide coordinates Absolute nucleotide coordinates etc... click hoxd11sod* tyrosine kinase receptor
Copyright OpenHelix. No use or reproduction without express written consent15 Multiple Matches click
Copyright OpenHelix. No use or reproduction without express written consent16 Sod2, at 10 kb Sod2 pick-list
Copyright OpenHelix. No use or reproduction without express written consent17 Sod2, at 1 Mb Sod2
Copyright OpenHelix. No use or reproduction without express written consent18 Reports and Analysis Perform actions and “Go” Download sequences or features Configure features with options Choose restriction sites
Copyright OpenHelix. No use or reproduction without express written consent19 WormBase and v1.69 New features in v1.69 description instructions search overview details tracks
Copyright OpenHelix. No use or reproduction without express written consent20 Display Quantitative Data “Wiggle” tracks display type Plot data with different values wiggle
Copyright OpenHelix. No use or reproduction without express written consent21 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent22 Annotation Controls: Tracks
Copyright OpenHelix. No use or reproduction without express written consent23 Selecting Tracks
Copyright OpenHelix. No use or reproduction without express written consent24 Changing Tracks
Copyright OpenHelix. No use or reproduction without express written consent25 Updated Image mouse over and click 2 transcripts 3 phenotypes 2 SNPs 4 targeted alleles pick-list
Copyright OpenHelix. No use or reproduction without express written consent26 Updated Image, at 1 Mb Sod2
Copyright OpenHelix. No use or reproduction without express written consent27 Configuring Tracks
Copyright OpenHelix. No use or reproduction without express written consent28 “Show” and “Format” Configurations pick-list
Copyright OpenHelix. No use or reproduction without express written consent29 “Expand & Label” View BEFOREAFTER Auto format Expand & Label format transcripts are labeled and expanded
Copyright OpenHelix. No use or reproduction without express written consent30 “Limit” and “Order” Configurations pick PAGE RELOADS pick
Copyright OpenHelix. No use or reproduction without express written consent31 Altering Track Order
Copyright OpenHelix. No use or reproduction without express written consent32 New Track Order Displayed Track 1
Copyright OpenHelix. No use or reproduction without express written consent33 Annotation Controls: Display Settings
Copyright OpenHelix. No use or reproduction without express written consent34 “Image Width”
Copyright OpenHelix. No use or reproduction without express written consent35 “Key Position” “Key” between annotations“Key” beneath annotations
Copyright OpenHelix. No use or reproduction without express written consent36 “Track Name Table” alphabetical Tracks varied Tracks
Copyright OpenHelix. No use or reproduction without express written consent37 “Grid” and “Highlight Features” now glyph GeneID:20656_Sod2 is yellow highlighted glyphs NM_013671_MGI:98352_Sod2 are yellow highlighted edit
Copyright OpenHelix. No use or reproduction without express written consent38 “Highlight Regions” edit highlights the specified region
Copyright OpenHelix. No use or reproduction without express written consent39 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent40 Add Your Own Tracks
Copyright OpenHelix. No use or reproduction without express written consent41 Add Your Own Tracks
Copyright OpenHelix. No use or reproduction without express written consent42 Sample Annotation Text File simple text file of annotations
Copyright OpenHelix. No use or reproduction without express written consent43 Uploading Personal Annotations Upload chemical annotations appear
Copyright OpenHelix. No use or reproduction without express written consent44 Configuring and Editing Your Own Tracks customize your glyphs to any color and shape
Copyright OpenHelix. No use or reproduction without express written consent45 Use any Data as an Annotation overlaid with TAF1 promoter binding skeleton phenotypes Discover genes that map to both sets of annotations.
Copyright OpenHelix. No use or reproduction without express written consent46 Add Remote Annotations
Copyright OpenHelix. No use or reproduction without express written consent47 Data Sharing: SNPedia --> HapMap GBrowse SNPedia data overlaid on HapMap GBrowse add remote URLs
Copyright OpenHelix. No use or reproduction without express written consent48 Bookmark and Share GBrowse
Copyright OpenHelix. No use or reproduction without express written consent49 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent50 WormBase Tour Data Source Expression data
Copyright OpenHelix. No use or reproduction without express written consent51 “Reports & Analysis” feature pick-list
Copyright OpenHelix. No use or reproduction without express written consent52 FlyBase Tour Data Source 12 fly genomes
Copyright OpenHelix. No use or reproduction without express written consent53 Comparative Genome Analysis C. elegans D. melanogaster orthologs
Copyright OpenHelix. No use or reproduction without express written consent54 HGSDD Tour Human Genome Segmental Duplication Database map genomic diseases to duplications disease duplications
Copyright OpenHelix. No use or reproduction without express written consent55 DictyBase Tour
Copyright OpenHelix. No use or reproduction without express written consent56 Personal Genomes jimwatsonsequence.cshl.edu jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence
Copyright OpenHelix. No use or reproduction without express written consent57 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent58 GBrowse: Universal & Unique GBrowse -- free software by GMOD -- standardize MODs -- universal and unique U N I V E R S A L A P P E A R A N C EU N I Q U E A P P E A R A N C E Tracks
Copyright OpenHelix. No use or reproduction without express written consent59 GBrowse: Sequences & Annotations intuitive searches genomic sequence annotated data
Copyright OpenHelix. No use or reproduction without express written consent60 GBrowse: Tracks & Customization choose data you want to see customize data the way you want to see it
Copyright OpenHelix. No use or reproduction without express written consent61 GBrowse: Add Your Data upload your own annotation files
Copyright OpenHelix. No use or reproduction without express written consent62 GBrowse: Tours Human Genome Segmental Duplication Database photo: NIH
Copyright OpenHelix. No use or reproduction without express written consent63 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse:
Copyright OpenHelix. No use or reproduction without express written consent64