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Ortholog and paralog information has been added to soybean data

09:14 27 March in Desktop Version
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We have loaded two versions of soybean genome. You now can compare individual chromosome pairs to see how genomic regions were rearranged during transition to the new version. Also, if you call Tools/Synteny matrix, you can see soybean genome duplication in a form of multiple dot plots. Just compare Wm81.a2.v1 to itself - select the same genome for both axes. [caption id="attachment_14898" align="alignleft" width="217"] Comparison of two versions of soybean chromosome 1.[/caption]...

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 https://persephonesoft.com/installation to see the installation instructions. [caption id="attachment_14865" align="alignright" width="300"] Syneteny matrix for comparison of sorghum and corn genomes. Each dot represents an ortholog pair[/caption]     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....

Persephone Presented at PAG

09:38 21 January in General News
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Many thanks to all the visitors who stopped by our booth at PAG, as well as those who attended Max Troukhan’s talk at the IRIC workshop. If you did not get a chance to see our demo, don’t worry -- a web-based version of Persephone is now freely available at http://web.persephonesoft.com. Currently, this version allows users to view and compare genomes of Oryza sativa ssp. japonica and Oryza sativa ssp. indica, as well as Arabidopsis thaliana, and the recently published version of Sorghum bicolor. If you have your favorite genome, please let us know and we will try to add it...

The Free Web Version Released

00:23 12 January in General News
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We are happy to announce that the first pilot version of Persephone for Web has been rolled out at http://web.persephonesoft.com. Our plan is to migrate the major functionality of the fully-featured commercial version to the free web application. For now, you can simultaneously view several maps with multiple tracks, smoothly zoom in all the way to the nucleotide level, align genetic and sequence maps linked by common markers, connect orthologous genes and thus visualize synteny between different species, run BLAST search and show results graphically. It is easier to overview the whole chromosomes when the maps are oriented vertically. If you prefer...

A Free Version of Persephone for Web

15:19 27 November in General News, Web Version
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We are exploring the new web technologies. Our first version of Persephone for Web will run in a browser using WebGL. Our first experiments have shown impressive results. The plan is to release it in December. The pilot version will work with public data and will be free for everyone. Any feedback is appreciated. [caption id="attachment_14730" align="alignnone" width="1024"] Comparison of two chromosomes of rice japonica and indica[/caption]  ...

Persephone at PAG

18:12 20 October in General News
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We will have a booth at Plant & Animal Genome conference in San-Diego. Please visit us at Town and Country Resort and Convention Center (Grand Exhibit Hall) between January 14 and January 16, 2018. In addition to that, we will give a 20 min talk at the International Rice Informatics Consortium workshop on January 17 between 10:30 AM and 12:40 PM. We are planning to go over the main features of Persephone genome viewer. Also, we will introduce the new version that runs in a web browser....