Genome Browsers

Hot Topic October 12, 2006

Overview

! Introduction ! UCSC Genome Browser

n  Options and custom annotation files ! Ensembl Genome Browser ! Other Browsers

n  ARGO n  Vista n  Gbrowse

Introduction

! Over 180 organisms sequenced ! Genome sizes range from a few kb to gbs

How do we extract visual information ! Genome characteristics:

n  Sequence features: GC content, repeats n  Annotation: predicted genes, ESTs n  Comparative genomics: syntenic regions,

conservered domains, SNPs, CNPs n  Resolution: Ideogram, basepair/triplets

Intro cont.

! Objective: n  Quick intro to a few browsers using a few

examples n  Details behind custom annotation files for the

UCSC browser n  A few tips on using the browsers

UCSC Genome Browser

UCSC Genome Browser ! Options:

n  Zoom in/out/base pair view n  Mapping and Sequencing Tracks

n  Genes and Gene Prediction Tracks

n  mRNA and EST Tracks

n  Expression and Regulation

n  Comparative Genomics

n  Variation and Repeats

*From UCSC genome browser

Custom Bed Files

! Browser Extensible Data ! Two components

n  Header – how your track will be displayed on the genome browser

n  Entries – information for each sequence feature you want visualized

Custom Bed Files: Header ! name=<track_label> - Defines the track label that will be displayed to the left of the

track up to 15 characters. ! description=<center_label> - Defines the center label.

! visibility=<display_mode> - Defines the initial display mode of the annotation track.

! color=<RRR,GGG,BBB> - Defines the main color for the annotation track. ! itemRgb=On - ! useScore=<use_score> -1 or 0 ! group=<group> default=user ! priority=<priority> - group order ! offset=<offset> - Defines a number to be added to all coordinates in the

annotation track. ! url=<external_url> - ! htmlUrl=<external_url> -

! Example: track name=joesESTmappings description=“Predicted ESTs” useScore=0

*From UCSC genome browser help pages

Custom Bed Files: Entry ! chrom - (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671). ! chromStart - The first base in a chromosome is numbered 0. ! chromEnd - The ending position of the feature in the chromosome or scaffold.

The chromEnd base is not included in the display of the feature. The 9 additional optional BED fields are:

! name - Defines the name of the BED line. ! score - A score between 0 and 1000. ! strand - Defines the strand - either '+' or '-'. ! thickStart - ! thickEnd - ! itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). ! blockCount - The number of blocks (exons) in the BED line. ! blockSizes - A comma-separated list of the block sizes. The number of items in

this list should correspond to blockCount. ! blockStarts - A comma-separated list of block starts. All of the blockStart

positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.

*From UCSC genome browser help pages

Custom Bed Files: Example name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On" chr7 127471196 127472363 Pos1 0 + 127471196 127472363 255,0,0 chr7 127472363 127473530 Pos2 0 + 127472363 127473530 255,0,0 chr7 127473530 127474697 Pos3 0 + 127473530 127474697 255,0,0 chr7 127474697 127475864 Pos4 0 + 127474697 127475864 255,0,0 chr7 127475864 127477031 Neg1 0 - 127475864 127477031 0,0,255 chr7 127477031 127478198 Neg2 0 - 127477031 127478198 0,0,255 chr7 127478198 127479365 Neg3 0 - 127478198 127479365 0,0,255 chr7 127479365 127480532 Pos5 0 + 127479365 127480532 255,0,0 chr7 127480532 127481699 Neg4 0 - 127480532 127481699 0,0,255

*From UCSC genome browser help pages

Ensembl Genome Browser

Ensembl Genome Browser

! Advantages n  Easy on the eyes n  Good interface to retrieving ensembl table

data ! Disadvantages

n  Slow Load up due to more functionality n  Interface isn’t as intuitive as UCSC browser

ARGO GB

ARGO GB

! Example

Vista GB

Vista GB

! Pluses n  Focused on pairwise comparisons between genomes n  Given a list of genes, will return all transcription

factors within 5kb of the TSS that were overrepresented in the gene set.(with p-values)

n  Track can be added to genome.ucsc.edu browser ! Negatives

n  No customization n  Limited annotation n  Limited interactivity

Gbrowse GB

Gbrowse GB

! Advantages n  Is your data not Public? n  Genome not complete or supported

! Still view your data on an internal genome browser ! Customize all tracks

! Disadvantages n  Setup time n  Maintanance n  Not as user friendly as other browsers, but still good!

Conclusion

! If you have sequence information, or an idea of how to extract it, we can visualize it.

! Comparing multiple genomes has become a widely used tool in determining important functional features.

! UCSC genome browser.