spring 2006, v7 copyright openhelix. no use or reproduction without express written consent 1 the...

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.

Copyright OpenHelix. No use or reproduction without express written consent 2

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


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


The UCSC Home page: genome.ucsc.edu

navigate

navigateGeneral information

Specific information—new features, current status, etc.


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


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


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


Overview of the wholeGenome Browser page

(first day, new human release)

}Genome viewer section

Track and image controls(day 1 = 40 tracks)


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


Different species, different tracks, same software


Sample Genome Viewer image, BRCA1 region

Genome backboneSTS markers

Known genes

RefSeq genes

Gene predictions

GenBank mRNAs

repeats

GenBank ESTs

conservation

SNPs

MGC clones


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


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


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


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


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…)


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


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


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


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.


•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


Agenda

Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene


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


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)


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


Proteome Browser

Access from homepage or Known Gene pages Exon diagram, amino acids Many protein properties (pI, mw, composition, 3D…)

moreprotein

data


Gene Sorter

Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser


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


Gene Sorter

From homepage select ‘Gene sorter’


Gene Sorter interface

Sorts genes by several criteria


Choose genome

Choose assembly

Type in gene nameor accession #




Choose from 11 sorting options



Configure display view



Filter data by different criteria


Gene Sorter results


Gene Sorter results

Obtain file of gene sequences or tab-delineated file of data


Table Browser







The Table Browser

Task:

Download sequence of all simple repeats of copy number more than 10 from a position on chromosome 4.


The Table Browser

From the Genome Browser home page, select Table Browser


Table browser: choose genome

Choose genome and assembly


Table browser: choose table to search

Data tables are organized by group & annotation track.


Table browser: choose region to search

Choose entire genome, ENCODE regions, enter a single position

or alternatively paste or upload a file of positions.


Table browser: filter to refine search

Filter is a form based sql query. Filters can be created for primary table and for related tables


Table browser: Output formats

Get fields of table data



Fasta file of sequence data



GTF or BED formated file



Custom track


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


Table browser: Output configuration


The Table Browser

Task:

Find simple repeats (copy number > 10) within known genes and download the sequence.


Table browser: Intersecting data

Intersect table with another table of data



Filtered simple repeats

Filtered simple repeats, intersected (overlapping) w/ known genes

Obtaining summary shows how intersecting narrowed search


Table browser: Correlating data


Custom Tracks







Custom Tracks: Table browser searches



Custom Tracks can be viewed in the Genome Browser



Custom tracks also are available for filtering and intersections on the Table Browser.


Intersecting previously created custom track finds one simple repeat with copy number >10 in known genes that also overlaps a CpG island.




Intersecting custom tracks with available data (or other custom tracks) can be a powerful discovery tool.


Custom Tracks







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


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


Custom Tracks: Format your Data

Bed Extensible Data


StartChromosome End Name Score Strand Thick start

Thick end

Color Blocks Block Sizes

Block starts



Define Genome Browser Characteristics (step 2)


browser position chr22:1000-10000browser pix 620browser hide allbrowser full gap

Default positionDefault image widthDefault track viewDefault track view



Define Track Characteristics (step 3)


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)



Upload and View your Track (step 4)


Custom Tracks







Custom Tracks from Outside Sources

Custom tracks list shared by the community


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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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

spring 2006, v7 copyright openhelix. no use or reproduction without express written consent 1 the...

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ucsc genome browser

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proteome browser

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