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The UCSC Genome Browser
Introduction
Materials prepared by
Mary Mangan, Ph.D.
www.openhelix.com
Updated: Q3 2008
Version13a_0708
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reproduction without express written
consent
3
Organization of Genomic Data
Annotation Tracks
sequence Genome backbone: base position number
chromosome band
sts sites
gap locations
known genes
predicted genes
Links out to
more data
microarray/expression data
evolutionary conservation
SNPs
repeated regions
more…
Copyright OpenHelix. No use or reproduction without express written consent
4
A Sample of the UCSC Genome Browser
gene details
official
sequence
Annotation Tracks
comparisons
SNPs
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UCSC Genome Browser Credits
Development team: http://genome.ucsc.edu/staff.html
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Led by David Haussler and Jim Kent
Dozens of staff and students bring you this software and data
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http://genome.ucsc.edu/goldenPath/credits.html
Funding, data sources, external contributors
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UCSC Genome Browser Agenda
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Introduction and Credits
Basic Searches
Understanding Displays
Get Details or Sequences
Sequence Searches (BLAT)
in silico PCR
Proteome Browser
VisiGene Browser
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
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The UCSC Homepage: http://genome.ucsc.edu
navigate
navigate
General information
Specific information—
new features, current status, etc.
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Genome Browser Gateway: start page, basic search
text/ID
searches
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Use this Gateway to search by:
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Gene names, symbols, IDs
Chromosome number: chr7, or region: chr11:1038475-1075482
Keywords: kinase, receptor
See lower part of page for help with format
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The Genome Browser Gateway
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Make your Gateway choices:
1.
Select Clade
2.
Select genome = species: search 1 species at a time
3.
Assembly: the official backbone DNA sequence
4.
Position: location in the genome to examine
5.
Image width: how many pixels in display window; 5000 max
6.
Configure: make fonts bigger + other choices
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The Genome Browser Gateway
sample search for Human TP53
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Sample search: human, March 2006 assembly, tp53
select
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Select from results list
ID search may go right to a viewer page, if unique
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}
Overview of the Whole
Genome Browser Page
Genome viewer section
(mature release)
Groups of data (Tracks)
Mapping and Sequencing Tracks
Phenotype and Disease Tracks
Genes and Gene Prediction Tracks
mRNA and EST Tracks
Expression and Regulation
Comparative Genomics
•As a group
•Individual species
Variation and Repeats
ENCODE Tracks
Copyright OpenHelix. No use or reproduction without express written consent
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Different Species, Different Tracks, Same Software
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Species may have different data tracks
Layout, software, functions the same
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Sample Genome Viewer Image, TP53 Region
base position
UCSC genes
RefSeq genes
MGC clones
mRNAs & ESTs
28 species compared
single species compared
SNPs
repeats
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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
For some tracks, the height of a bar is increased likelihood
of an evolutionary relationship (conservation track)
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Options for Changing Images: Upper Section
Walk
left or
right
Zoom
in
Specify
a
position
Zoom
out
fonts,
window,
more
click to
zoom 3x
and re-center
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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…
Copyright OpenHelix. No use or reproduction without express written consent
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Annotation Track Display Options
enforce
changes
Links to info
and/or filters
Change
track view
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Some data is ON or OFF by default
Menu links to info about the tracks: content, methods
You change the view with pulldown menus
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After making changes, REFRESH to enforce the change
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Copyright OpenHelix. No use or reproduction without express written consent
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Annotation Track options, defined
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Hide: removes a track from view
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Dense: all items collapsed into a single line
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Squish: each item = separate line, but 50% height + packed
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Pack: each item separate, but efficiently stacked (full height)
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Full: each item on separate line
Copyright OpenHelix. No use or reproduction without express written consent
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Reset, Hide, Configure or Refresh to Change Settings
Flip display to
Genomic 3’5’
reset, back
to defaults
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enforce any changes
(hide, full, squish…)
start from
scratch
You control the views
Use pulldown menus
Configure options page
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Cookies and Sessions
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Your browser remembers where you were (cookies)
OR
To clear your “cart” or parameters, click default tracks or reset
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Save your setup as “sessions” and store/share them
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Click Any Viewer Object for 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
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informative
description
other resource links
links to sequences
Click Annotation Track Item
for Details 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
mRNA descriptions
pathways
gene model
Copyright OpenHelix. No use or reproduction without express written consent
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Get DNA, with Extended Case/Color Options
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Copyright OpenHelix. No use or reproduction without express written consent
Use the DNA link at
the top
Plain or Extended
options
Change colors,
fonts, etc.
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Get Sequence from Details Pages
Click a track, go to Sequence section of details page
Click the item
sequence section
on detail page
Copyright OpenHelix. No use or reproduction without express written consent
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UCSC Genome Browser Agenda
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Introduction and Credits
Basic Searches
Understanding Displays
Get Details or Sequences
Sequence Searches (BLAT)
in silico PCR
Proteome Browser
VisiGene Browser
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
25
Accessing the BLAT Tool
BLAT = BLAST-like Alignment Tool
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Rapid searches by INDEXING the entire genome
Works best with high similarity matches
See documentation and publication for details
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Kent, WJ. Genome Res. 2002. 12:656
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BLAT Tool Overview:
www.openhelix.com/sampleseqs.html
Make
choices
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Paste one
or more
sequences
DNA limit 25000 bases
Protein limit 10000 aa
25 total sequences
submit
Or
upload
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sorting
Results with demo sequences, settings default; sort = Query, Score
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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)
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BLAT Results: Browser
query
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From browser click in BLAT results
A new line with Your Sequence from BLAT Search appears!
Base position = “full” menu and zoomed in enough to see
amino acids in 3 frame translation
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BLAT Results,
Alignment Details
Your query
Genomic match, color cues
Side-by-side alignment
yours
genomic
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30
UCSC Genome Browser Agenda

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


Introduction and Credits
Basic Searches
Understanding Displays
Get Details or Sequences
Sequence Searches (BLAT)
in silico PCR
Proteome Browser
VisiGene Browser
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
31
In-Silico PCR:
Find Genomic Sequence using Primers
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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)
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32
In-Silico PCR Results
location
size
your primers
Tm for primers
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Genomic location shown, links to Genome Viewer
Product size shown
Your primers displayed, flipped if necessary
Predicted genomic sequence shown
Primer melting temperatures provided
Copyright OpenHelix. No use or reproduction without express written consent
33
Proteome Browser
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Access from homepage or
UCSC Gene pages
Exon diagram, amino acids…
Many protein properties (pI,
mw, composition, 3D…)
more
data
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34
VisiGene Image Browser
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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 consent
35
UCSC Genome Browser Agenda

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Introduction and Credits
Basic Searches
Understanding Displays
Get Details or Sequences
Sequence Searches (BLAT)
in silico PCR
Proteome Browser
VisiGene Browser
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
36
Hands-on session for basic searches
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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 consent
37
Notice:

The materials and slides offered are for non-commercial use only.
Reproduction, distribution and/or use for commercial purposes is
strictly prohibited.

Copyright 2006, OpenHelix, LLC

http://www.openhelix.com/ucscmaterials.shtml
Copyright OpenHelix. No use or reproduction without express written consent
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