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SynMap: Whole Genome Syntenic Dotplots
   
   
Please Note:
SynMap is a very computationally intense, multi-step program which may take hours to complete for large genomes.
If available, select previously run parameter-sets for your organisms to see results instantly.
Get Started:
Click here for an example analysis between Arabidopsis thaliana and Arabidopsis lyrata.
(Note that syntenic gene pairs are colored by synonymous mutations (kS))
Click here for an explaination of the results.
Generate SynMap Clear Results
Organism 1 Search:
Name: Description:
Organism count: 7415
Genome:
Organism 2 Search:
Name: Description:
Organism count: 7415
Genome:
Default distance settings for:
Average distance expected between syntenic genes (-g):
Maximum distance between two matches (-D):
Minimum number of aligned pairs (-A): genes
Download DAGChainer
Blast Algorithm:
Regenerate dotplot images?
Dotplot axis metric:
Master image width (0 == dynamic)
Minimum chromosome size:
Calculate substitution rates for syntenic protein coding gene pairs and color syntenic dots accordingly (slow)?
Order contigs by best syntenic path?
E-mail results?
Previously run parameters: Hide
(Clicking on row automatically selects and sets SynMap genomes and parameters.)
    

Currently logged in as: public 2009-11-23 16:51:18
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