BITS: UCSC genome browser - Part 1

Paco Hulpiau

UCSCgenome browsing

http://www.bits.vib.be

Introduction

§ Browse genes in their genomic context

§ See features in and around a specific gene

§ Investigate genome organization and explore larger

chromosome regions

§ Search and retrieve information on a gene- and

genome-scale

§ Compare genomes

Introduction

§ Collaboration between main genome browsers

Ensembl, UCSC and NCBI

» use same genome assemblies

» interlinking between sites

§ Ensembl Genome Browser: http://www.ensembl.org/

§ NCBI Map Viewer: http://www.ncbi.nlm.nih.gov/mapview/

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

Introduction

Introduction

Introduction

Introduction

Introduction

Introduction

§ Collaboration between main genome browsers

Ensembl, UCSC and NCBI

» use same genome assemblies

» interlinking between sites

§ Ensembl Genome Browser: http://www.ensembl.org/

§ NCBI Map Viewer: http://www.ncbi.nlm.nih.gov/mapview/

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

Introduction

Introduction

Introduction

§ Collaboration between main genome browsers

Ensembl, UCSC and NCBI

» use same genome assemblies

» interlinking between sites

§ Ensembl Genome Browser: http://www.ensembl.org/

§ NCBI Map Viewer: http://www.ncbi.nlm.nih.gov/mapview/

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

Introduction

Introduction

Introduction

Introduction

§ Other genome browsers and genome databases:

http://genome.jgi-psf.org Eukaryotic (143) and prokaryotic (505) genomes

http://www.xenbase.org Xenopus tropicalis

http://flybase.org Drosophila genes & genomes

http://www.wormbase.org C. elegans and some related nematodes

http://www.tigr.org => http://www.jcvi.org/ Comprehensive Microbial Resource (CMR) => http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://genolist.pasteur.fr Microbial genomes

Introduction

Introduction

§ The UCSC Genome browser was created by the

Genome Bioinformatics Group

at the University of California Santa Cruz (UCSC).

http://genome.ucsc.edu/

§ The Genome Browser zooms and scrolls

over chromosomes, showing the work of

annotators worldwide.

§ Blat quickly maps your sequence to the genome.

BLAT is not BLAST !

BLAT works by keeping an index of the entire genome in memory.

The index consists of all non-overlapping DNA 11-mers or protein 4-mers.

The index is used to find areas of probable homology, which are then

loaded into memory for a detailed alignment.

BLAT on DNA can quickly find sequences of 95% and greater similarity

of length 40 bases or more.

BLAT on proteins finds sequences of 80% and greater similarity of length

20 amino acids or more.

§ The Table Browser provides convenient

access to the underlying database.

§ The Gene Sorter displays a sorted table of genes

that are related to one another.

The relationship can be one of several types, including protein-

level homology,

similarity of gene expression profiles,

or genomic proximity.

§ In-Silico PCR searches a sequence database with a pair of PCR

primers, using an indexing strategy for fast performance.

§ When successful, the search returns a file (fasta) containing all

sequences in the database that lie between and include the

primer pair.

§ Genome Graphs is a tool for displaying

genome-wide data sets such as the results

of genome-wide SNP association studies,

linkage studies and homozygosity mapping.

§ Galaxy allows you to do analyses you cannot do

anywhere else without the need to install or

download anything.

§ You can analyze multiple alignments, compare

genomic annotations and much more...

§ VisiGene lets you browse through a large

collection of in situ mouse and frog images.

§ The Proteome Browser provides a wealth of

protein information presented in the form of

graphical images of tracks and histograms

and links to other sites.

§ The Utilities page contains links to some tools

created by the UCSC Genome Bioinformatics Group.

§ DNA Duster & Protein Duster remove non-sequence

related characters from an input sequence.

§ The Utilities page contains links to some tools

created by the UCSC Genome Bioinformatics Group.

§ DNA Duster & Protein Duster remove non-sequence

related characters from an input sequence.

Clade – Genome - Assembly

GENOMEBROWSERDISPLAY

POSITIONCONTROL

TRACK CONTROL

Navigation: position control

Navigation: position control

§ Click the zoom in and zoom out buttons on top

to zoom in or out 1.5, 3 or 10-fold

on the center of the window

Navigation: position control

§ Zoom in 3-fold by clicking anywhere

on the base position track

§ Zoom to a specific region using “drag and zoom”

Navigation: position control

§ To scroll the view of the display horizontally

by set increments of 10%, 50% or 95%

of the displayed size (as given in base pairs)

click the corresponding move arrow

Navigation: position control

§ To scroll the left of right side by a specified number of

vertical gridlines while keeping the opposite side fixed

click the appropriate move start or move end

arrow

Navigation: position control

§ To display a (completely) different position

enter the new location in the position/search text

box

§ You can also jump to an other gene location

Annotation Tracks

TRACK CONTROL

HIDE = removes a track from view

FULL = each item on a separate line

DENSE = all items collapsed into single line

SQUISH = all items on several lines PACKED and at 50% height

PACK = each item separate and efficiently stacked (full height)

Annotation Tracks

Annotation Tracks

§ Different genome/assembly => different tracks!

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

§ Now try to change the tracks as follows

Annotation Tracks

§ and...

SQUISH

PACK

FULL

DENSE

SQUISH

UTR EXON

INTRON

direction of transcription

EXON

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Annotation Tracks

Browser graphics in PDF

TABLE BROWSER

GET DNA

CLICK LINE

CURRENT BROWSER GRAPHIC IN PDF

TO GET OTHER DATA

CURRENT BROWSER GRAPHIC IN PDF

TO GET OTHER DATA

1

Exercises (I)

1) Search for your gene of interest

on Human Feb. 2009 (GRCh37/hg19) Assembly

» Include 1000 base pairs up- and downstream

» Only show the tracks:

RefSeq Genes (pack)

Conservation (full, primates only)

» Save graphical view as PDF (exercises1_1)

Exercises (I)

2) How many transcripts are there?

» Compare UCSC Genes with RefSeq and Ensembl genes!

» Save graphical view as PDF (exercises1_2)

Exercises (I)

3) What are the flanking genes?

Are these conserved outside mammals?

» Zoom out until you can see at least

two or three flanking genes

(may need to hide some tracks, leave RefSeq on)

» Now have a look in the chicken genome

» Save graphical view as PDF

(exercises1_3a en exercises1_3b)

Exercises (I)

4) Is there any regulatory information available?

» Change the view to see the genomic region upstream

(exon 1 and ~2000 upstream) and open some regulatory tracks

e.g. ORegAnno, TFBS Conserved, TS miRNA sites

» Save graphical view as PDF (exercises1_4)