spring 2006, v7 copyright openhelix. no use or reproduction without express written consent 1 the...
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Spring 2006, v7 Copyright OpenHelix. No use or reproduction without express written consent
1
The UCSC Genome Browser
Search, retrieve and displaythe data that you want
UCSC Genome Browser TrainingSpring 2006
Part 1
Materials developed by:Warren C. Lathe, Ph.D.
Mary Mangan, Ph.D.
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UCSC Genome Browser credits
Led by David Haussler and Jim Kent Dozens of staff and students also work to bring you this
software and data
Development team: http://genome.ucsc.edu/staff.html
http://genome.ucsc.edu/goldenPath/credits.html Funding, data sources, external contributors
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Agenda
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom
Tracks
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The UCSC Home page: genome.ucsc.edu
navigate
navigateGeneral information
Specific information—new features, current status, etc.
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The Genome Browser Gatewaystart page, basic search
text/ID searches
Helpful search examples,
suggestions below
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 format
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The Genome Browser Gatewaystart page choices, February 2005
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
5. Image width: how many pixels in display window; 5000 max
6. Configure: make fonts bigger + other choices
1 2 43 5
6
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The Genome Browser Gatewaysample search for Human BRCA1
Sample search: human, May 2004 assembly, BRCA1
•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
select
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Overview of the wholeGenome 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 wholeGenome Browser page
(mature release)
}Genome viewer section
mRNA and EST Tracks
Expression and Regulation
Comparative Genomics
ENCODE Tracks Variation and Repeats
Groups of dataMapping and Sequencing Tracks
Genes and Gene Prediction Tracks
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Different species, different tracks, same software
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Sample Genome Viewer image, BRCA1 region
Genome backboneSTS markers
Known genes
RefSeq genes
Gene predictions
GenBank mRNAs
repeats
GenBank ESTs
conservation
SNPs
MGC clones
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Visual Cues on the Genome Browser
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
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Options for changing the images: upper section
Change your view with controls at the top Use “base” to get right down to the nucleotides Configure: 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 options
Some data is ON or OFF by default
Links to detailsand/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, defined Hide: 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 settings
You control the view Use pulldown menus Configure options page
reset, back to defaults to start
from scratch
enforce the changes (hide, full, squish…)
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Annotation Track options, if altered….important point: the browser remembers!
Session information (the position you were examining) Track choices (squish, pack, full, etc) Filter parameters (if you changed the colors of any items, or the
subset to be displayed)
…are all saved on your computer. When you come back in a couple of days to use it again, these will still be set. You may—or may not—intend this.
To clear your “cart” or parameters, click default tracks
OR
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Clicking an annotation line, new page of detailed information
You will get detail for that single item you clickExample: 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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Click annotation track = BRCA1 “Known gene” detail page informative
description
other resource links
microarray data
mRNA secondary structure
links to sequences
protein domains/structure
homologs in other species
Gene Ontology™ descriptions
mRNA descriptions
pathways
Not all genes have This much detail.
Different annotation tracks
carry different detaildata.
SNP detail page
sample
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Getting the sequencesGet DNA, with Extended Options; or Details pages
Use the DNA link at the top
Plain or Extended options
Change colors, fonts, etc.
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•Genomic (many options) •mRNA•Protein
Getting the sequencesAnother way: from details pages
Click a track, go to Sequence section of details page
Click the line
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Agenda
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom
Tracks
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In Silico PCR: find genomic sequence using primers
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
Genomic location shown, links to Genome Viewer
location your primers
Your primers displayed, flipped if necessary Predicted genomic sequence shown
Tm for primers
Primer melting temperatures provided
size
Product size shown
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Proteome Browser
Access from homepage or Known Gene pages Exon diagram, amino acids Many protein properties (pI, mw, composition, 3D…)
moreprotein
data
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Gene Sorter
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks
Table Browser Searches User-generated Data Externally Generated Data
Hands-on session for Sorter, Table Browser, and Custom Tracks
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Gene Sorter
From homepage select ‘Gene sorter’
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Gene Sorter interface
Sorts genes by several criteria
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Choose genome
Choose assembly
Type in gene nameor accession #
Gene Sorter interface
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Gene Sorter interface
Choose from 11 sorting options
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Gene Sorter interface
Configure display view
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Gene Sorter interface
Filter data by different criteria
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Gene Sorter results
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Gene Sorter results
Obtain file of gene sequences or tab-delineated file of data
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Table Browser
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks
Table Browser Searches User-generated Data Externally Generated Data
Hands-on session for Sorter, Table Browser, and Custom Tracks
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The Table Browser
Task:
Download sequence of all simple repeats of copy number more than 10 from a position on chromosome 4.
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The Table Browser
From the Genome Browser home page, select Table Browser
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Table browser: choose genome
Choose genome and assembly
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Table browser: choose table to search
Data tables are organized by group & annotation track.
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Table browser: choose region to search
Choose entire genome, ENCODE regions, enter a single position
or alternatively paste or upload a file of positions.
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Table browser: filter to refine search
Filter is a form based sql query. Filters can be created for primary table and for related tables
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Table browser: Output formats
Get fields of table data
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Table browser: Output formats
Fasta file of sequence data
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Table browser: Output formats
GTF or BED formated file
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Table browser: Output formats
Custom track
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Table browser: Obtaining output
Output as file or in browser. Also, obtain statistics.
Adding name creates file on desktop,leaving blank creates output in browser. (exception: custom track)
Obtain a summary of specified data
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Table browser: Output configuration
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The Table Browser
Task:
Find simple repeats (copy number > 10) within known genes and download the sequence.
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Table browser: Intersecting data
Intersect table with another table of data
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Table browser: Intersecting data
Filtered simple repeats
Filtered simple repeats, intersected (overlapping) w/ known genes
Obtaining summary shows how intersecting narrowed search
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Table browser: Intersecting data
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Table browser: Correlating data
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Custom Tracks
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks
Table Browser Searches User-generated Data Externally Generated Data
Hands-on session for Sorter, Table Browser, and Custom Tracks
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Custom Tracks: Table browser searches
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Custom Tracks: Table browser searches
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Custom Tracks: Table browser searches
Custom Tracks can be viewed in the Genome Browser
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Custom Tracks: Table browser searches
Custom tracks also are available for filtering and intersections on the Table Browser.
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Intersecting previously created custom track finds one simple repeat with copy number >10 in known genes that also overlaps a CpG island.
Custom Tracks: Table browser searches
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Custom Tracks: Table browser searches
Intersecting custom tracks with available data (or other custom tracks) can be a powerful discovery tool.
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Custom Tracks
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks
Table Browser Searches User-generated Data Externally Generated Data
Hands-on session for Sorter, Table Browser, and Custom Tracks
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Custom Tracks: User-generated Data
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Custom Tracks: User-generated Data
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Custom Tracks: User-generated Data
Four steps in creating a custom annotation track Format your data Define Genome Browser characteristics Define annotation track characteristics Upload and view your track
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Custom Tracks: Format your Data
Format Your Data (step 1)
GFFGTFPSLBEDWIG
Browser Extensible Data
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
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Custom Tracks: Format your Data
Bed Extensible Data
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
StartChromosome End Name Score Strand Thick start
Thick end
Color Blocks Block Sizes
Block starts
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Custom Tracks: User-generated Data
Define Genome Browser Characteristics (step 2)
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
browser position chr22:1000-10000browser pix 620browser hide allbrowser full gap
Default positionDefault image widthDefault track viewDefault track view
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Custom Tracks: User-generated Data
Define Track Characteristics (step 3)
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
browser position chr22:1000-10000browser pix 620browser full gap
track name=pairedReads description="Clone Paired Reads" visibility=3 color=0,128,0 useScore=1
Default track visibility0=hide1=dense2=full3=pack4=squish
Default track color Score on (1) or off (0)
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Custom Tracks: User-generated Data
Upload and View your Track (step 4)
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Custom Tracks: User-generated Data
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Custom Tracks: User-generated Data
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Custom Tracks: User-generated Data
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Custom Tracks: User-generated Data
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Custom Tracks: User-generated Data
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Custom Tracks
Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks
Table Browser Searches User-generated Data Externally Generated Data
Hands-on session for Sorter, Table Browser, and Custom Tracks
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Custom Tracks from Outside Sources
Custom tracks list shared by the community
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References for the UCSC Genome BrowserGeneral Browser topics: Hinrichs, A.S. et. al (2006). The UCSC Genome Browser Database:
update 2006:. Nucl. Acids Res. 34(Database issue), D590-8. Kent, W.J., Sugnet, C. W., Furey, T. S., Roskin, K.M., Pringle, T. H., Zahler, A. M.,
and Haussler, D. (2002). The Human Genome Browser at UCSC. Genome Res. 12:996-1006.
Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., Weber, R.J., Haussler, D. and Kent, W.J. (2003). The UCSC Genome Browser Database. Nucl. Acids Res 31:51-54.
BLAT: Kent, W.J. (2002). BLAT - The BLAST-Likse Alignment Tool. Genome Res.
12:656-664.
Table Browser: Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D.
and Kent, W.J. (2004). The UCSC Table Browser data retrieval tool. Nucleic Acids Research, 2004, Vol. 32, Database issue D493-D496.
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Join the mailing list!
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Additional Materials available: www.openhelix.com
UCSC sponsored material at www.openhelix.com/ucscmaterials.shtml Frequently updated training presentation and
exercises Self-run tutorial Quick Reference Cards
Tutorials and web seminars on a number of other tools Additional sponsored bioinformatics tools coming soon