Transcript OpenHelix LLC tutorials - UNC Health Sciences Library

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The UCSC Genome Browser
Additional Tools
Materials prepared by
Warren C. Lathe III, Ph.D.
Mary Mangan, Ph.D.
www.openhelix.com
Updated: Q3 2008
Version14c_0908
Copyright OpenHelix. No use or
reproduction without express written
consent
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UCSC Genome Browser Agenda
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Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
4
The UCSC Homepage: http://genome.ucsc.edu
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UCSC Genome Browser Agenda
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Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
6
Gene Sorter
From homepage
select “Gene Sorter”
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7
Gene Sorter Example
Sort genes by
similarity criteria
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8
Gene Sorter: Chose Genome and Gene
Type in gene name
Choose Assembly
Choose Genome
or accession number
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9
Gene Sorter: Similarity Sorting Options
Choose from several
similarity sorting options,
varies by assembly & species
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10
Gene Sorter: Configure
Configure
Choose order of
display columns
Choose columns of
data to display
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Some columns can
be configured
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Gene Sorter: Saving Configuration
Configure
Hide, show all columns
or return to default
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Save configurations
and load previous
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Gene Sorter: Adding Custom Data
Configure
Custom data
Custom columns of
user’s data
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13
Gene Sorter: Filters
List genes
Filter
Filter data of columns
displayed or those
not displayed
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List all genes found
with selected filters
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Gene Sorter: Save Filters
Save filter
trim_name
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Click save
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Gene Sorter: Load Filters
Saved filters
Choose filter & load
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Gene Sorter: Submit Filters
Submit
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Gene Sorter: Get Results
Go to results
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Gene Sorter: Sort Results by Name
Description
Re-sort
Re-sort genes based on
gene clicked using same
parameters.
Copyright OpenHelix. No use or reproduction without express written consent
19
Gene Sorter: VisiGene Results
VisiGene
Open UCSC VisiGene
image page for gene.
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20
Gene Sorter: Alignment Results
Alignment Amino
acid alignment
between reference gene
and gene protein products
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21
Gene Sorter: Open Genome Browser
Open Genome Browser
to location of chosen
gene
Browser
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22
Gene Sorter: Open Details Page
Open gene details
page of chosen gene
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Description
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Gene Sorter: Gene Sequences
Sequences
Get sequences
Choose sequence type,
obtain FASTA file of
all gene sequences
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24
Gene Sorter: Text File of Data
Data text
Obtain tab-delineated
file of all displayed
gene data
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25
Gene Sorter
Sort genes by
similarity criteria
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26
UCSC Genome Browser Agenda







Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
27
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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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
29
UCSC Genome Browser Agenda







Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
30
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…
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VisiGene Results
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List of results
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Select one to view
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Links and details
Copyright OpenHelix. No use or reproduction without express written consent
32
UCSC Genome Browser Agenda







Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
33
Proteome Browser
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Collection of protein level data
Access from homepage or UCSC Gene pages
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Proteome Browser Results
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Protein level data
Exons illustrated, link to browser
Domains, family
Structure
Pathways
Copyright OpenHelix. No use or reproduction without express written consent
35
UCSC Genome Browser Agenda







Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
36
Other Features
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Utilities: other small useful tools
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liftOver: to migrate between genome versions
Dusters: to clean up stray characters in
sequence files
Tree Maker
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37
Explore!
genomewiki.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
38
UCSC Genome Browser Agenda







Introduction
Gene Sorter
in silico PCR
VisiGene Browser
Proteome Browser
Other Features
Exercises
UCSC Genome Browser: http://genome.ucsc.edu
Copyright OpenHelix. No use or reproduction without express written consent
39
Hands-on session for UCSC Additional Tools
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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
40
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

http://www.openhelix.com/ucsc
Copyright OpenHelix. No use or reproduction without express written consent
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