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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…
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A sample of what we will find:
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The UCSC Home page: genome.ucsc.edu
navigate
General information
navigate
Specific information—
new features, current status, etc.
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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…
See lower part of page for help with format
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The Genome Browser Gateway
start page choices, February 2005
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Make your Gateway choices:
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Select Clade
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Select 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
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Image width: how many pixels in display window; 5000 max
6.
Configure: make fonts bigger + other choices
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The Genome Browser Gateway
sample search for Human BRCA1
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Sample search: human, May 2004 assembly, BRCA1
select
•Often you will have to select the
right gene from a results list
•Sometimes, you will go directly
to a browser image (use an ID)
•AF005068, breast cancer 1, early onset
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Overview of the whole
Genome Browser page
(first day, new human release)
}
Genome viewer section
Track and image controls
(day 1 = 40 tracks)
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Overview of the whole
Genome Browser page
(mature release)
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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
ENCODE Tracks
Variation and Repeats
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Different species, different tracks, same software
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Sample Genome Viewer image, BRCA1 region
Genome backbone
STS markers
Known genes
RefSeq genes
MGC clones
Gene predictions
GenBank mRNAs
GenBank ESTs
conservation
SNPs
repeats
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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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Clicking an annotation line,
new page of detailed information
You will get detail for that single item you click
Example: click on the BRCA1 Black “Known Genes” line
Click the line
New
web page
opens
Many details
and links
to more data
about BRCA1
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informative
description
Click annotation track = BRCA1
“Known gene” detail page
other resource links
links to sequences
microarray data
Not all genes have
This much detail.
Different
annotation tracks
carry different detail
data.
mRNA secondary structure
protein domains/structure
homologs in other species
SNP
detail page
sample
Gene Ontology™ descriptions
mRNA descriptions
pathways
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Getting the sequences
Get DNA, with Extended Options; or Details pages
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Use the DNA link at
the top
Plain or Extended
options
Change colors,
fonts, etc.
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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
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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
Or
upload
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Submit
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BLAT results, with links
sorting
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Results with demo sequences, settings default; sort = Query, Score
 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)
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BLAT results, alignment details browser
Click to flip frame
query
matches
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From browser click in BLAT results
A new line with your Sequence from BLAT Search appears!
Watch out for reading frame! Click - - - > to flip frame
Base position = full and zoomed in enough to see
amino acids
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BLAT results,
alignment details
Your query
Genomic match, color cues
Side-by-side alignment
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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
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Proteome Browser
more
protein
data
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Access from homepage or Known Gene pages
Exon diagram, amino acids
Many protein properties (pI, mw, composition, 3D…)
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Gene Sorter
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From homepage select ‘Gene sorter’
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Gene Sorter interface
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Sorts genes by several criteria
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Gene Sorter interface
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Choose from 11 sorting options
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Gene Sorter results
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