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satsuma website  

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Environment Modules

Run module spider satsuma to find out what environment modules are available for this application.

System Variables

  • HPC_SATSUMA_DIR - installation directory
  • HPC_SATSUMA_BIN - executable directory
  • HPC_SATSUMA_EXE - sameple directory


If you publish research that uses satsuma you have to cite it as follows:

Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.