the genome genome browser training materials developed by: warren c. lathe, ph.d. and mary mangan,...

The Genome

Genome Browser Training

Materials developed by:Warren C. Lathe, Ph.D. and Mary Mangan, Ph.D.

[email protected]

Part 1

Organization of genomic data…

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 will find:

Agenda

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 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 backbone

STS markers

Known genes

RefSeq genes

Gene predictions

GenBank mRNAs

repeats

GenBank ESTs

conservation

SNPs

CCDS

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

Change track view

You change the view with pulldown menus

enforcechanges

After making changes, REFRESH to enforce the change

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




Tracks

Accessing the BLAT tool

Rapid searches by INDEXING the entire genome Works best with high similarity matches See documentation and publication for details

BLAT = BLAST-like Alignment Tool

BLAT tool overview: www.openhelix.com/sampleseqs.html

Submit

Make choices

DNA limit 25000 basesProtein limit 10000 aa25 total sequences

Paste one or more

sequences

Or upload

BLAT results, with links

Results with demo sequences, settings default; sort = Query, Score Score is a count of matches—higher number, better match

sorting

Click browser to go to Genome Browser image location (next slide) Click details to see the alignment to genomic sequence (2nd slide)

BLAT results, alignment details browser

From browser click in BLAT results A new line with your Sequence from BLAT Search appears!

query

matches

Click to flip frame

Watch out for reading frame! Click - - - > to flip frame Base position = full and zoomed in enough to see

amino acids

BLAT results,alignment details

Your query

Genomic match, color cues

Side-by-side alignment

Agenda




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

Agenda




Tracks

Hands-on session for basic searches

Exercises on the handouts We will walk through them together 2 styles: questions only, and step-by-step When we are finished the formal exercises, we can

help you to investigate issues that you want to understand for your research

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


the genome genome browser training materials developed by: warren c. lathe, ph.d. and mary mangan,...

Documents

browser image

data slide

custom tracks slide

genome browser track

genome browser text

gene prediction tracks

software slide

format slide