Transcript Browsing the Genome

Browsing the Genome
Using Genome Browsers to
Visualize and Mine Data
Genome Browsers
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Software designed to enable a user to
access and display sequence data
Provide a visual correlation for different
types of information
Organize large amounts of genome
sequence data
Several Different Genome Browsers
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Common features:
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Coordinate system is based on the build
Zoom in and out
Gene features aligned to genome
Major Differences:
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Each Browser has a very different look and feel
Navigating through the information
Main Genome Browser Repositories
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Ensembl
NCBI (Entrez) - BLAST
UCSC - BLAT
Ensembl, NCBI, and UCSC use the same
human genome assembly that is
generated by NCBI but release timing is
different between sites
UCSC
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Vertebrates, Deuterostomes, Insects,
Nematodes, Yeast
Entry into genome sequence via BLAT
Table Browser
Creation of PDF
Provides access to all the data produced by the
project, and to the software used to analyze and
present it
Site produces and maintains annotation tracks
Aligned Annotation Tracks
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Genomic data: known genes, predicted genes,
ESTs, mRNAs, CpG islands, assembly gaps and
coverage, chromosomal bands, mouse
homologies, and more
Annotation tracks are both computed at UCSC
from publicly available sequence data and
provided by collaborators
Users can also add their own custom tracks to
the browser
UCSC Outline
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Navigating
Configuring Browser
Extracting data
Home Page
BLAT
BLAT Results
Standard Query
Query Results
Graphical Interface
Configuring Display
Components
Get DNA
Configuring DNA
DNA STS Highlighted
Tracks
Track Display
Human SDAD1
Convert
Mouse Sdad1
EST Track
Entry Data
Viewing Exons
Integrate Specific Data
Custom Tracks
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User provided annotation data
Can be in standard GFF format or in a
format designed specifically for UCSC
Genome Browser, including GTF, PSL, BED,
WIG, and microarray (BED15)
Add Custom Tracks
Sample Custom Tracks
GFF
chr5 EST exon 92719127 92719406 . + 0 BE
chr5 EST exon 92731587 92731784 . + 0 BE
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Bed
chr5 92715320 92715326 miR-194 1 chr5 92715467 92715474 miR-124.1 3 chr5 92715467 92715473 miR-124/506 1 
Display of Custom Tracks
Configure Track Display
Save PDF
Table Browser
Sample Table Data
Proteome Browser
Protein Sequence
Protein Characteristics
Structure Information
Summary of UCSC
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Different ways of querying genome
Control over graphical display
Vast amount of genomic data
Ability to collect that data
However
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UCSC does not include my genome
Actually no genome browser supports my
genome
Custom Browser Software
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GBrowse is a combination of database and
interactive Web page for manipulating and
displaying annotations on genomes
Annotation Browsers- Argo and Apollo