Transcript UCSC Genome Browser

Genomes at NCBI
Genomes at NCBI
Database and Tool Explosion
The annual database
issue of NAR (Nucleic Acids
Research) has grown
exponentially
2009: 1170 databases
and tools
2000: 230 databases
and tools
1996: first annual
compilation of
databases and tools
lists 57 databases and
tools
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Genome Browsers
UCSC
Genome Browser
EBI
Ensembl
NCBI
Map Viewer
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Organizing the Genome
Gene X
genes & predictions
variations and
mutations
Description
Transcript data
Structure
Gene Ontology
Pathway Data
Homologous
Genes
Expression Data
Etc….
cross-species
comparative data
and many more types of data from expression
and regulation to mRNA and ESTs…
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UCSC Genome Browser: genome.ucsc.edu
UCSC Genome
Browser
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gene details
Annotation Tracks
official
sequence
comparisons
SNPs
A sample of what we can find:
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The 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
Chromosome number: chr7, or region: chr11:1038475-1075482
Keywords: kinase, receptor
IDs: NP, NM, OMIM, and more…
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The Genome Browser Gateway
start page choices, December 2006
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Make your Gateway choices:
1. Select Clade
2. Select species: search 1 species at a time
3. Assembly: the official backbone DNA sequence
4. Position: location in the genome to examine
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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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Overview of the whole
Genome Browser page
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Genome viewer section
Groups of data
Mapping and Sequencing Tracks
Genes and Gene Prediction Tracks
mRNA and EST Tracks
Expression and Regulation
Comparative Genomics
Variation and Repeats
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Sample Genome Viewer image,
TP53 region
base position
STS markers
Known genes
17 species compared
single species compared
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Options for Changing Images:
Upper Section
Walk
left or
right
click to
zoom 3x
and re-center
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Zoom
in
Zoom
out
Specify
a
position
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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Annotation Track display options
enforce
changes
Links to info
and/or filters
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Some data is ON or OFF by default
Change
track view
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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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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
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Reset, Hide, Configure or Refresh to change
settings
enforce any changes
(hide, full, squish…)
reset, back
to defaults
start from
scratch
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Click Any Viewer Object for Details
Click the item
New
web page
opens
Example: click your
mouse anywhere
on the TP53 line
Many details
and links
to more data
about TP53
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informative
description
other resource links
Click annotation track item
for details pages
links to sequences
microarray data
Not all genes have
this much detail.
mRNA secondary structure
protein domains/structure
homologs in other species
Gene Ontology™ descriptions
mRNA descriptions
pathways
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Get DNA, with Extended Case/Color Options
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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 line
Click the item
sequence section
on detail page
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Accessing the BLAT tool
BLAT = BLAST-like Alignment Tool
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BLAT tool overview:
Make
choices
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Paste one
or more
sequences
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go to alignment detail
go to browser/viewer
BLAT results, with links
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BLAT results, browser link
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BLAT results,
alignment details
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Proteome Browser
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Access from homepage or
Known Gene pages
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Exon diagram, amino
acids…
Many protein properties
(pI,
mw, composition, 3D…)
more
data
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In-Silico PCR:
Find genomic sequence using primers
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