genome browsers - massachusetts institute of...
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Genome Browsers
Hot Topic October 12, 2006
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Overview
! Introduction ! UCSC Genome Browser
n Options and custom annotation files ! Ensembl Genome Browser ! Other Browsers
n ARGO n Vista n Gbrowse
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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
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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
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UCSC Genome Browser
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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
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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
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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
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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
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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
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Ensembl Genome Browser
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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
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ARGO GB
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ARGO GB
! Example
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Vista GB
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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
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Gbrowse GB
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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!
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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.