Blog

Wheat RH Genetic Maps Have Been Loaded

12:14 24 July in Web Version
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We have uploaded the wheat RH Maps (from IWGSC) with marker positions in cM. Persephone automatically links maps by common markers, so, if you align a chromosome map based on sequence with a corresponding genetic map, the tracks with markers on both maps will appear to be connected. The same visualization, based on orthologous gene pairs, is also available for revealing the synteny between chromosomes of wheat and rice. In wheat, if you align A chromosomes vs. B chromosomes, you can visualize similarity and structural rearrangements between them. See this in action: https://web.persephonesoft.com/?bookmark=E1736B7E3EB3401319D28EB0BD97722A [caption id="attachment_14943" align="aligncenter" width="399"] Two pairs of sequence-based maps are...

Wheat Genome Data from IWGSC Have Been Released

15:07 09 July in Web Version
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According to wheatgenome.org, all data related to the reference sequence of bread wheat, IWGSC RefSeq v1.0, are available without restriction. We would like to use this opportunity to demonstrate the abilities of the web version of Persephone, a tool specifically designed to deal with large data sets, such as the wheat genome. We just have uploaded the reference sequences assembled into 22 pseudo-chromosomes (14 Gbp) and one annotation track with gene models. The search index and BLAST database are being updated. We plan to populate the database with new tracks on a daily basis, please check it out....

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 http://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...