Ucscintro Slides V23a

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The UCSC Genome Browser

Introduction
Materials prepared by
Mary Mangan, Ph.D.
www.openhelix.com
Version 23a_0114
Copyright OpenHelix. No use or

reproduction without express written
consent
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

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
A Sample of the UCSC Genome Browser

gene details
reference
sequence
Annotation Tracks
comparisons
SNPs
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

Basic Searches
Summary
Exercises

The UCSC Homepage: http://genome.ucsc.edu

navigate
navigate
General information
Specific information
new features, current status, etc.
Gateway: Start Page for a Basic Search

text/ID
searches
l es
p
m
pf
l
e
H
m
for
Use this Gateway to search:
xa
e
ch vided
r
a
e ro
ul s at p
Gene names, symbols, IDs

Chromosome number: chr7, or region: chr11:1038475-1075482
Keywords: kinase, receptor
See lower part of page for help with format

10
UCSC Genome Browser Gateway

1
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
11
Sample Search for Human TP53
select
Sample search: human, February 2009 assembly, tp53
uc002gij.3
Select from results list; or goes to a viewer page, if unique

12

Basic Searches
Summary
Exercises

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
Literature, Publications
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)

14
Different Assemblies, Species, Tracks
Assemblies, Species may have different data tracks

Layout, software, functions the same
15
Sample Genome Viewer Image, TP53 Region

scale
base position
UCSC genes
RefSeq
Publications
mRNAs & ESTs
ENCODE
many species compared
single species compared
SNPs
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 meaningfor 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
Vert.
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
17
Options for Changing Images: Upper Section

walk
zoom
Tweak position
or do new search
Drag (like Google Maps)
Rightclick
items
Hold/drag mouse
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
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
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)
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
21
Mid-page Options to Change Settings

Search for
data types
Flip display to
Genomic 53
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
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
23

Basic Searches
Summary
Exercises

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

25
informative
description
other resource links
links to sequences
Click Annotation Track Item

for Description Pages
genetic association
studies
comparative toxicology
common gene haplotype alleles
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
GeneReviews
gene model
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.
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

28

Basic Searches
Summary
Exercises

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

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
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 matcheshigher 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)
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
33
BLAT Results, Alignment Details

Your query
Genomic
match, with
color cues
Side by Side Alignment
yours
genomic
34

Basic Searches
Summary
Exercises

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
36

Basic Searches
Summary
Exercises

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
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 2014, OpenHelix, LLC
http://www.openhelix.com/ucscintro
39

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Copyright OpenHelix.

No use or reproduction without express written consent

Important note to slide users:

To maintain the color schemes/cues and the animations, if you

The UCSC Genome Browser

Copyright OpenHelix. No use or

UCSC Genome Browser Agenda

Introduction and Credits

UCSC Genome Browser: http://genome.ucsc.edu

Organization of Genomic Data

sequence Reference genome: base position number

A Sample of the UCSC Genome Browser

Copyright OpenHelix. No use or reproduction without express written consent

UCSC Genome Browser Credits

Led by David Haussler and Jim Kent

Copyright OpenHelix. No use or reproduction without express written consent

UCSC Genome Browser Agenda

Introduction and Credits

UCSC Genome Browser: http://genome.ucsc.edu

The UCSC Homepage: http://genome.ucsc.edu

Copyright OpenHelix. No use or reproduction without express written consent

Gateway: Start Page for a Basic Search

Use this Gateway to search:

Gene names, symbols, IDs

See lower part of page for help with format

UCSC Genome Browser Gateway

Make your Gateway choices:

Sample Search for Human TP53

Sample search: human, February 2009 assembly, tp53

Select from results list; or goes to a viewer page, if unique

UCSC Genome Browser Agenda

Introduction and Credits

UCSC Genome Browser: http://genome.ucsc.edu

Overview of the Whole

(2009 Human Assembly)

Groups of data (Tracks)

Variation and Repeats

(including SNPs, copy number variation)

Different Assemblies, Species, Tracks

Assemblies, Species may have different data tracks

Sample Genome Viewer Image, TP53 Region

Visual Cues on the Genome Browser

< exon < < < <ex 5' UTR

Intron and direction of transcription <<< or >>>

Options for Changing Images: Upper Section

Drag (like Google Maps)

Change your view or location with controls at the top

Annotation Track Display Options

Some data is ON or OFF by default

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

Tracks with Additional Options: Filters, more.

Mid-page Options to Change Settings

Search for data types

Cookies and Sessions

Your browser remembers where you were (cookies)

Save your setup as Session and store/share them

Copyright OpenHelix. No use or reproduction without express written consent