Genomics and Personalized Care in Health Systems

Lecture 5 Genome Browser

Leming Zhou, PhDSchool of Health and Rehabilitation Sciences

Department of Health Information Management

Genome Browser• Genome Browser is a computer program which helps to

display gene maps, browse the chromosomes, align genes or gene models with ESTs or contigs etc.

• Big Three:– UCSC Genome Browser – NCBI Mapviewer– Ensemble

UCSC Genome Browser: http://genome.ucsc.edu

NCBI Mapviewer

Ensemble

The UCSC Genome Browser

Slides adopted from OpenHelix training materials

UCSC Genome Browser• http://genome.ucsc.edu

Genome Browser Gateway• Use this Gateway to search by:

– Gene names, symbols, IDs– Chromosome number: chr7, or region: chr11:1038475-1075482– Keywords: kinase, receptor

• See lower part of page for help with format

Genome Browser Gateway

The Genome Browser Gateway

Make your Gateway choices:1. Select Clade2. Select genome = 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

4 51 32

assembly

6

The Genome Browser Gateway

• Sample search: human, March 2006 assembly, tp53

select

Select from results list ID search may go right to a viewer page, if unique

Sample Genome Viewer Image, TP53 Region

base position

UCSC genes

RefSeq genes

mRNAs & ESTs

repeats

many species compared

SNPs

single species compared

MGC clones

Visual Cues on the Genome Browser

Track colors may have meaning—for example, UCSC Gene track:• If there is a corresponding PDB entry = black• If there is a corresponding reviewed/validated seq = dark blue• If there is a non-RefSeq seq = lightest blue

Tick marks; a single location (STS, SNP)

For some tracks, the height of a bar is increased likelihood of an evolutionary relationship (conservation track)

Intron and direction of transcription <<< or >>>

<exon exon exon< < < < < < <ex 5' UTR3' UTR

Alignment indications (Conservation pairs: “chain” or “net” style)• Alignments = boxes, Gaps = lines

Options for Changing Images: Upper Section

• Change your view or location with controls at the top• Use “base” to get right down to the nucleotides• Configure: to change font, window size, more…

– Next item, next exon navigation assistance can be turned on

Specifya

position

Fonts,window,

next item,more

Walkleft orright

Zoomin

Zoomout

Click tozoom 3x

and re-center

Annotation Track Display Options

• Some data is ON or OFF by default• Menu links to info about the tracks: content, methods• You change the view with pulldown menus• After making changes, REFRESH to enforce the change

enforcechange

s

Enforcechanges

Change track view

Links to infoand/or filters

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

Pack: each item separate, but efficiently stacked (full height)

Full: each item on separate line

Mid-page Options to Change Settings

• You control the views• Use pulldown menus• Configure options page

Reset, back to defaults Start from

scratch

Enforce any changes (hide, full, squish…)

Flip display to Genomic 3’5’

Cookies and Sessions• Your browser remembers where you were (cookies)

To clear your “cart” or parameters, click default tracks or reset

OR

Save your setup as “sessions” and store/share them

Click Any Viewer Object for Details

Example: click your mouse anywhere on the TP53 line

Click the item

New description web page opens

Many details and links

to more data about TP53

Get DNA, with Extended Case/Color Options• Use the DNA link at

the top• Plain or Extended

options• Change colors, fonts,

etc.

Base Level and Protein Sequences

BLASTX Search to Confirm the Protein

Get Sequence from Details Pages

Click a track, go to Sequence section of details page

Click the item

sequence sectionon detail page

Accessing the BLAT Tool

• BLAT = BLAST-like Alignment Tool– Rapid searches by INDEXING the entire genome– Works best with high similarity matches

BLAT• BLAT on DNA is designed to quickly find sequences of 95% and

greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 25 bases, and sometimes find them down to 20 bases.

• BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.

• In practice DNA BLAT works well on primates, and protein BLAT on land vertebrates

• BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats.

• http://genome.ucsc.edu

BLAT Search

Make choices

DNA limit 25000 basesProtein limit 10000 aa

25 total sequences

Paste one or more sequences

Or upload

submit

BLAT Results with Hyperlinks

• 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

BLAT Results: Browser

• From browser click in BLAT results• A new line with Your Sequence from BLAT Search appears! Base position = “full” menu and zoomed in enough to see amino acids

in 3 frame translation

query

BLAT Results,Alignment Details

Your query

Genomic match, color cues

Side by Side Alignment

yoursgenomic

Summary

• UCSC Genome Browser• Visual cues and genomic context• Many ways to alter your views• Access to deeper data• Access and use sequence data

UCSC Table Browser

The Table Browser

Open browser

Open browser

Table Browser

34

Many Other Databases Use UCSC Genome Browser Mirror and Software

• Malaria: http://areslab.ucsc.edu/• Arabidopsis: http://epigenomics.mcdb.ucla.edu/• Archaea: http://archaea.ucsc.edu/• GSID HIV Browser: http://www.gsid.org/• GEP Drosophila Genome Browser: http://gander.wustl.edu• …

GEP Drosophila Genome Browser• UCSC Genome Browser, GEP version, parts of genomes, GEP

data, used for annotation of Drosophila species

– http://gander.wustl.edu

Male Drosophila melanogasterhttp://en.wikipedia.org/wiki/Drosophila_melanogaster

Drosophila melanogaster Chromosomes

http://en.wikipedia.org/wiki/Drosophila_melanogaster

Fruit Flies and Human Disease Research• About 75% of known human disease genes have a

recognizable match in the genetic code of fruit flies, and 50% of fly protein sequences have mammalian analogues.

• An online database called Homophila is available to search for human disease gene homologues in flies and vice versa.

• Drosophila is being used as a genetic model for several human diseases including the neurodegenerative disorders Parkinson's, Huntington's, spinocerebellar ataxia and Alzheimer's disease.

• The fly is also being used to study mechanisms underlying aging and oxidative stress, immunity, diabetes, and cancer, as well as drug abuse.

Homework 4• Read through the BLAST tutorial (IntroToBLAST.zip, A simple Introduction

to NCBI BLAST) and follow the instructions to reproduce the results described in the tutorial. List the steps you have taken and indicate whether you find any differences from the results mentioned in the tutorial.

• Use the sequence of BRCA1 gene, run a BLAT search against human genome (the most recent assembly, GRCh37), select the best sequence alignment result and view the output in the genome browser. You should provide a screen shot of the obtained page, which should include at least the gene, its homolog genes, other refseq, mRNA, the gene in other species, SNPs, and repeats. – Obtain mRNA-Genomic Alignments record from the browser– Obtain the predicted protein sequence from the browser– Obtain the precise location of one SNP record in the genome sequence– Zoom in to the base level and determine the protein sequence corresponding to

one well conserved exon; get the DNA sequence of the exon, run a blastx search (do not apply low complexity filtering) to confirm the correctness of the protein sequence you obtain