gmod/gbrowse_syn
DESCRIPTION
GMOD/GBrowse_syn. Sheldon McKay iPlant Collaborative DNA Learning Center Cold Spring Harbor Laboratory. Outline. A few words on whole genome alignment A brief survey of synteny browsers A few challenges of rendering comparative data Comparative genome browsing with GBrowse_syn. - PowerPoint PPT PresentationTRANSCRIPT
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GMOD/GBrowse_syn
Sheldon McKayiPlant CollaborativeDNA Learning CenterCold Spring Harbor Laboratory
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A few words on whole genome alignment
A brief survey of synteny browsers
A few challenges of rendering comparative data
Comparative genome browsing with GBrowse_syn
Outline
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Hierarchical Genome Alignment Strategy
Mask repeats (RepeatMasker, Tandem Repeats Finder, nmerge, etc
Identify orthologous regions (ENREDO, MERCATOR, orthocluster, etc)
Nucleotide-level alignment (PECAN, MAVID, etc)
Further processing
GBrowse_syn
GBrowse_syn
GBrowse
Raw genomic sequences
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A Few Use Cases
Multiple sequence alignment data from whole genomes
Synteny or co-linearity data without alignments
Gene orthology assignments based on proteins
Self vs. Self comparison of duplications, homeologous regions, etc
Others
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What is a Synteny Browser?
- Has display elements in common with genome browsers
- Uses sequence alignments, orthology or co-linearity data to highlight different genomes, strains, etc.
- Usually displays co-linearity relative to a reference genome.
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A Brief Survey of GMOD-friendly Synteny Browsers*
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Wang H, Su Y, Mackey AJ, Kraemer ET and JC Kissinger . SynView: a GBrowse-compatible approach to visualizing comparative genome data Bioinformatics 2006 22:2308-2309
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Pan, X., Stein, L. and Brendel, V. 2005. SynBrowse: a Synteny Browser for Comparative Sequence Analysis. Bioinformatics 21: 3461-3468
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Crabtree, J., Angiuoli, S. V., Wortman, J. R., White, O. R. Sybil: methods and software for multiple genome comparison and visualization Methods Mol Biol. 2007 Jan 01; 408: 93-108.
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+ others...
Youens-Clark K, Faga B, Yap IV, Stein LD, Ware, D. 2009. CMap 1.01: A comparative mapping application for the Internet. doi:10.1093
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GBrowse_syn
+others…McKay SJ, Vergara IA and Stajich, J. 2010. "Using the Generic Synteny Browser (Gbrowse_syn)" in Current Protocols in Bioinformatics (Wiley Interscience) doi: 10.1002/0471250953.bi0912s31
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GMOD Browser branding/nomenclature issues…
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Other non-GMOD Browsers
http://mkweb.bcgsc.ca/circos/ http://www.mizbee.org
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Other non-GMOD Browsers
http://synteny.cnr.berkeley.edu/CoGe/
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Apologies to others not listed
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How is GBrowse_syn different?
• Does not rely on perfect co-linearity across the entire displayed region (no orphan alignments)
• Offers “on the fly” alignment chaining• No upward limit on the number of species• Used grid lines to trace fine-scale indels (sequence
insertion/deletions)• Integration with GBrowse data sources• Ongoing support and development
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GBrowse-like interface
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GBrowse Databases*
*.synor
*.conf
*.synconf
GBrowse_synalignment database
GBrowse_syn
Species config. Master config.
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GBrowse_syn Architecture[GBrowse]
[GBrowse] [GBrowse]
[GBrowse]
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Getting Data into GBrowse_syn
CLUSTALW PECANMSF ad hoc tab-delimitedFASTA STOCKHOLM GFF3 etc…
Loading scripts
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Optional “All in one” view
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Adding markup to the annotations
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Problem : How to use Insertions/Deletion data
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Tracking Indels with grid lines
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Evolution of Gene Structure
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Putative gene or loss
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Comparing gene models
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Comparing assemblies
Not bad
Needs work
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Example Mercator Alignment
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Getting the most out of small aligned regions or orthology-only data
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Gene Orthology
Chained Orthologs
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2 panels mergedInversion + translocation?
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What about synteny blocks that fall off the ends of the displayed reference sequence?
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Solution 1 : With multiple sequence alignment data, calculate many anchor points (done anyway for grid lines)
Solution 2 : For orthology-based synteny blocks, use individual start and end coordinates of orthologs as anchor points.
Solution 3: If all else fails, guess the end of the target block based on the overall length ratio.
length displayed target = (length target/length reference)* length displayed reference
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What if the aligned DNA sequences are too distant?
!=
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Pecan alignments
Protein orthology based Synteny blocks
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What about segmental duplications?
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The Future of GBrowse_syn
• Full Integration with GBrowse 2
• “On the fly” sequence alignment view
• AJAX-based user interface and navigation (Jbrowse_syn)
• Suggestions?
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Acknowledgments
Lincoln SteinDave Clements
Scott CainJason Stajich
Bonnie HurwitzEva Huala
Cynthia LeeJack Chen
Ismael VergaMichael Paulini
WormBase Curators
Richard Hayes Rob Buels
Projects Funding