SyMAP Synteny Browser
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SyMAP (Synteny Mapping and Analysis Program) v4.0 is an automated system for identifying and displaying genome synteny alignments. The genomes may be represented by sequenced chromosomes (pseudomolecules), by draft sequence contigs, or by FPC physical maps (with BAC-end or marker sequence).

If you use results from this page in a publication or website, please reference:
        Soderlund, et al. (2011) Nucl. Acids Res. doi:10.1093/nar/gkr123 (link).


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This project is supported by the National Research Initiative of USDA's National Institute of Food and Agriculture, grant #0214643.
Sample Multi-Genome Alignments

SyMAP was developed for analysis of eudicots and monocots, but has also been tested on mammalian, bacterial, and fungal genomes. Note that the applet may load slowly the first time, since the Java files must be downloaded. If the applet runs out of memory, follow these steps.

NOTE: Java version 7 has enhanced security. If Java does not give you access to the applet, you will need to go to the

NOTE: Displays are for demonstration purposes; genomes may not be most current versions.

Select a group to view the synteny in SyMAP v4.0
Poaceae Maize, Rice, Brachypodium, Sorghum
Fabaceae, et al. Arabidopsis, Medicago, Soy, Poplar, Grape
Rosaceae, Curcurbiteae Apple, Peach, Cucumber

  • All alignments were computed using default SyMAP parameters.
  • Genomes were not repeat masked prior to analysis.
  • MUMmer and Blat were used to compute the raw anchors. Nucleotide alignment was used for all of the FPC alignments and plant genome self-alignments, all others used protein alignment.