UCSC Genome Browser UCSC Genome Browser 1
Feb 21, 2016
UCSC Genome BrowserUCSC Genome Browser
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The ProgressThe Progress
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Data from NCBI and TIGR(www.ncbi.nlm.nih.gov and www.tigr.org )
Official “15 year”Human Genome Project:
1990-2003
Today - 85,759,586,764
Database and Tool ExplosionDatabase and Tool Explosion
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2000: 230 databases and tools listed in compilation1996: first annual
compilation of databases and tools lists 57 databases and tools
The annual databaseissue of Nucleic AcidsResearch has grownexponentially
2008: 1078 databases and tools listed in compilation
NCBIMap ViewerEBI
Ensembl
Genome BrowsersGenome Browsers
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UCSCGenome Browser
Organizing the GenomeOrganizing the Genome
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genes & predictions
variations and repeats
cross-speciescomparative data
and many more types of data from expressionand regulation to mRNA and ESTs…
Gene X
DescriptionTranscript dataStructureGene OntologyPathway DataHomologous GenesExpression DataEtc….
UCSC Genome Browser: genome.ucsc.eduUCSC Genome Browser: genome.ucsc.edu
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UCSC Genome UCSC Genome BrowserBrowser
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Organization of genomic data…Organization of genomic data…
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Genome backbone: base position numbersequenceA
nnot
atio
n Tr
acks
chromosome band
known genespredicted genes
evolutionary conservationSNPs
sts sitesgap locations
repeated regions
microarray/expression data
more…
Links out to more data
A sample of what we will find:A sample of what we will find:9
gene details
comparisons
SNPs
Ann
otat
ion
Trac
ks
officialsequence
The Genome Browser GatewayThe Genome Browser Gatewaystart page, basic searchstart page, basic search
Use this Gateway to search by:◦ 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 format10
text/ID searches
Helpful search examples,
suggestions below
The Genome Browser GatewayThe Genome Browser Gatewaystart page choices, December 2006start page choices, December 2006
Make your Gateway choices:1. Select Clade2. Select species: search 1 species at a time3. Assembly: the official backbone DNA sequence4. Position: location in the genome to examine5. Image width: how many pixels in display window; 5000
max6. Configure: make fonts bigger + other choices
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1 4 5
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2 3
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The Genome Browser GatewayThe Genome Browser Gatewaysample search for Human TP53sample search for Human TP53
Sample search: human, March 2006 assembly, tp53
select
Select from results list ID search may go right to a viewer page, if unique
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Overview of the wholeOverview of the wholeGenome Browser pageGenome Browser page
}Genome viewer section
mRNA and EST Tracks
Expression and Regulation
Comparative Genomics
Variation and Repeats
Groups of data
Mapping and Sequencing Tracks
Genes and Gene Prediction Tracks
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Sample Genome Viewer image, Sample Genome Viewer image, TP53 regionTP53 region
base positionSTS markers
Known genes
RefSeq genesGenBank seqs
repeats
17 species compared
SNPs
single species compared
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Visual Cues on the Genome Visual Cues on the Genome BrowserBrowser
Track colors may have meaning—for example, Known Gene track:•If there is a corresponding PDB entry, = black•If there is a corresponding NCBI Reviewed seq, = dark blue•If there is a corresponding NCBI Provisional seq, = light blue
Tick marks; a single location (STS, SNP)
Intron, and direction of transcription <<< or >>>
<exon exon exon< < < < < < <ex 5' UTR3' UTR
For some tracks, the height of a bar is increased likelihoodof an evolutionary relationship (conservation track)
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Options for Changing Images: Options for Changing Images: Upper SectionUpper Section
Change your view or location with controls at the top
Use “base” to get right down to the nucleotidesConfigure: to change font, window size, more…
Specifya
position
fonts,window,
more
Walkleft orright
Zoomin
Zoomout
click tozoom 3x
and re-center
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Annotation Track display optionsAnnotation Track display options
Some data is ON or OFF by default
Links to infoand/or filters
Menu links to info about the tracks: content, methods You change the view with pulldown menus
enforcechanges
After making changes, REFRESH to enforce the change
Change track view
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Annotation Track options, definedAnnotation Track options, definedHide: 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
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Reset, Hide, Configure or Refresh to change Reset, Hide, Configure or Refresh to change settingssettings
You control the viewsUse pulldown menusConfigure options page
reset, back to defaults start from
scratch
enforce any changes (hide, full, squish…)
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Click Any Viewer Object for DetailsClick Any Viewer Object for Details
Example: click your mouse anywhere on the TP53 line
Click the item
New web page
opens
Many details and links to more data about TP53
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Click annotation track item Click annotation track item for details pages for details pages
Not all genes have This much detail.
Different annotation tracks
carry different data.
informativedescriptionother resource links
microarray data
mRNA secondary structure
links to sequences
protein domains/structure
homologs in other species
Gene Ontology™ descriptions
mRNA descriptions
pathways
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Get DNA, with Extended Case/Color OptionsGet DNA, with Extended Case/Color Options
Use the DNA link at the top
Plain or Extended options
Change colors, fonts, etc.
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Get Sequence from Details PagesGet Sequence from Details PagesClick a track, go to Sequence section of details page
Click the line Click the item
sequence sectionon detail page
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Accessing the BLAT toolAccessing the BLAT tool
Rapid searches by INDEXING the entire genome
Works best with high similarity matchesSee documentation and publication for details
◦ Kent, WJ. Genome Res. 2002. 12:656
BLAT = BLAST-like Alignment Tool
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BLAT tool overview: BLAT tool overview:
Make choices
DNA limit 25000 basesProtein limit 10000 aa25 total sequences
Paste one or more
sequences
Or upload
submit
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BLAT results, with linksBLAT results, with links
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)
sorting
go to
bro
wse
r/vie
wer
go to
alig
nmen
t det
ail
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BLAT results, BLAT results, browser linkbrowser link
From browser click in BLAT resultsA new line with your Sequence from BLAT Search
appears!
query
click to flip frame
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,BLAT results,alignment alignment detailsdetails
Your query
Genomic match, color cues
Side-by-side alignment
yoursgenomic
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Proteome BrowserProteome Browser
Access from homepage or Known Gene pages
Exon diagram, amino acids…
Many protein properties (pI, mw, composition, 3D…)
more data
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In-Silico PCR: In-Silico PCR: Find Find genomicgenomic sequence using primers sequence using primers
Select genomeEnter primersMinimum 15
basesFlip reverse
primer?Submit