UCSC Genome BrowserUCSC Genome Browser

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The ProgressThe Progress

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Database and Tool ExplosionDatabase and Tool Explosion

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2000: 230 databases and tools

1996: first annual compilation of databases and tools lists 57 databases and tools

The annual databaseissue of Nucleic AcidsResearch has grownexponentially

2009: 1170 databases and tools

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….

Ensembl: www.ensembl.orgEnsembl: www.ensembl.org

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Ensembl – Human Y chromosomeEnsembl – Human Y chromosome

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NCBI Map NCBI Map ViewerViewer

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NationalCenter forBiotechnologyInformation(NIH)

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 T

rack

s

chromosome band

known genes

predicted genes

evolutionary conservation

SNPs

sts sites

gap locations

repeated regions

microarray/expression data

more…

Links out to more data

A sample of what we can find:A sample of what we can find:12

gene details

comparisons

SNPs

An

nota

tion

Tra

cks

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 format13

text/ID searches

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

6

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 genes

GenBank 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.

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 Pages

Click 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

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

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BLAT results, with linksBLAT results, with links

go

to b

row

ser/

vie

we

r

go

to a

lign

me

nt d

eta

il

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BLAT results, BLAT results, browser linkbrowser link

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BLAT results,BLAT results,alignment alignment detailsdetails

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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