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Tools in Bioinformatics
Genome Browsers
Retrieving genomic information
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Previous lesson(s): annotation-based
perspective of search/data
Today: genomic-based perspective: look at
all the data from the prism of a specific
chromosome location
Next: sequence-based searches
Genome browsers
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NCBI Map Viewer
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Ensembl
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http://www.ncbi.nih.gov/mapview
http://www.ensembl.org/
UCSC Genome Browser
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http://genome.ucsc.edu/
Important note to slide users:
PC users
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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
5
The UCSC Genome Browser
Introduction
Materials prepared by
Mary Mangan, Ph.D.
www.openhelix.com
Updated: Q1 2009
Version16a_0209
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)
Summary
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
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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
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A Sample of the UCSC Genome Browser
gene details
official
sequence
Annotation Tracks
comparisons
SNPs
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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)
Summary
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
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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
12
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
Copyright OpenHelix. No use or reproduction without express written consent
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The Genome Browser Gateway
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assembly
Make your Gateway choices:
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Select Clade
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Select genome = species: search 1 species at a time
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Assembly: the official backbone DNA sequence
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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
Copyright OpenHelix. No use or reproduction without express written consent
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The Genome Browser Gateway
sample search for Human TP53
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Sample search: human, March 2006 assembly, tp53
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Select from results list
ID search may go right to a viewer page, if unique
select
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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)
Summary
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
16
}
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
(including sno/miRNA data)
mRNA and EST Tracks
Expression (such as microarray)
Regulation (including TFBS)
Comparative Genomics
•As a group
•Individual species
Variation and Repeats
(including SNPs, copy number variation)
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
Copyright OpenHelix. No use or reproduction without express written consent
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Sample Genome Viewer Image, TP53 Region
base position
UCSC genes
RefSeq genes
MGC clones
mRNAs & ESTs
many species compared
single species compared
SNPs
repeats
Copyright OpenHelix. No use or reproduction without express written consent
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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)
Alignment indications (Conservation pairs: “chain” or “net” style)
•Alignments = boxes, Gaps = lines
Copyright OpenHelix. No use or reproduction without express written consent
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Options for Changing Images: Upper Section
Walk
left or
right
Zoom
in
Specify
a
position
Click to
zoom 3x
and re-center
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Zoom
out
Fonts,
window,
next item,
more
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…
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Next item, next exon navigation assistance can be turned on
Copyright OpenHelix. No use or reproduction without express written consent
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Annotation Track Display Options
Enforce
enforce
changes
Links to info
and/or filters
Change
track view
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Some data is ON or OFF by default
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Menu links to info about the tracks: content, methods
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You change the view with pulldown menus
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After making changes, REFRESH to enforce the change
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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Mid-page Options 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
Copyright OpenHelix. No use or reproduction without express written consent
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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
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)
Summary
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
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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
Copyright OpenHelix. No use or reproduction without express written consent
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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)
Summary
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
31
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
Copyright OpenHelix. No use or reproduction without express written consent
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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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Copyright OpenHelix. No use or reproduction without express written consent
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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)
Copyright OpenHelix. No use or reproduction without express written consent
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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
Copyright OpenHelix. No use or reproduction without express written consent
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BLAT Results,
Alignment Details
Your query
Genomic match, color cues
Side by Side Alignment
yours
genomic
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
Introduction Summary
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UCSC Genome Browser
Visual cues and genomic context
Many ways to alter your views
Access to deeper data
Access and use sequence data
Copyright OpenHelix. No use or reproduction without express written consent
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