A Trial Version of Persephone for Windows is Open for Download

A Trial Version of Persephone for Windows is Open for Download

17:19 01 March in Desktop Version, General News
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We released a trial version of Persephone for Windows. It has many more features than the web version. In fact, it is a full production version with  just a couple of features temporarily disabled. We plan to enable the rest of the functionality later this month. Please visit http://persephonesoft.com/installation to see the installation instructions.

Syneteny matrix for comparison of sorghum and corn genomes. Each dot represents an ortholog pair

 

 

The data set has many plant genomes from public sources:

  • Arabidopsis thaliana (TAIR10)
  • Brachypodium distachyon (Bd21)
  • Brassica napus (Chalhoub et. al 2014)
  • Glycine max (Wm82.a2.v1)
  • Medicago truncatula (Mt4.0)
  • Oryza sativa ssp. indica (ASM465v1.28)
  • Oryza sativa ssp. japonica (IRGSP-1.0.25, MSU_osa1r7)
  • Solanum licopersicum (SL2.40)
  • Sorghum bicolor (Sbi1)
  • Zea mays (B73 RefGen_v1, B73 RefGen_v2).
Sorghum chromosome 9 in the middle is aligned vs. chromosome 6 and 8 of corn

Sorghum chromosome 9 in the middle is aligned vs. chromosome 6 and 8 of corn

 

When compared, they show a good synteny. For example, try to align sorghum and rice (Oryza sativa japonica) genomes. Sorghum chromosome 3 aligns nicely with rice chromosome 1. You can also see a genome duplication between sorghum and corn.

We also added the human and mouse genomes, just in case you are not so much interested in plants.

This page should give you a good quick start. Please let us know what you think. Thank you