Blog

Potato genome data added to the Windows demo version

14:18 05 March in Desktop Version
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We have uploaded the version DM_v4.03 of the potato genome (Solanum tuberosum). Here is the list of tracks: Gene models predicted by GLEAN Public mRNA and EST from NCBI for potato were aligned to the genomic sequences using hisat2. This track shows experimental support for the predicted genes, allowing the users to see if the predicted splice sites and exon structure is consistent with the transcript sequences. DArT marker mapping. Unambiguously mapped Potato Diversity Arrays Technology (DArT) marker sequences. OPA marker mapping.  Dundee-derived SNP marker positions on the PGSC Version 4.03 Pseudomolecules used for the Dundee oligo-nucleotide pooled assay (OPA)...

NCBI’s Gnomon annotation track has been added to human genome GRCh38 data set

17:22 04 March in Web Version
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A new track with the latest annotation by NCBI's Gnomon (Feb.2019) pipeline has been added to Homo sapiens GRCh38 data set. See the bottom track on this picture. The gene models are sometimes quite different from the models in other tracks. Use the evidence tracks, like the conservation scoring phylop100way (the red-blue histogram above), to see which prediction looks more convincing....

Potato DM_v4.03 and tomato SL3.0 genomes have been added

22:25 21 February in Web Version
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We have loaded the potato genome (DM_v4.03) with multiple annotation tracks showing gene models, mapped markers and repeats. To help assessing the gene prediction quality, we downloaded 300,000 potato EST and mRNA sequences from NCBI and splice-aligned them to the genome. This produced a track with transcripts showing exact location of active splice sites. Most of the predicted genes are consistent with the alignments, though some of them have serious problems (see the locus on the left): Another Solanum species, tomato (version SL3.0), has also been added to the database. Connecting the orthologous tomato and potato genes shows a good synteny between...

Persephone at PAG XXVII – 2019

11:34 27 January in General News
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This was our second year attending the largest Ag-Genomics meeting in the world in San Diego CA. Many thanks to all who stopped by our exhibit as well as those who attended Max Troukhan's talk at the IWGSC workshop (https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/36359) where he demonstrated the wheat genome data visualized in Persephone. We had a steady stream of visitors to our booth all of whom had sincere interest in our product. The interactions that we had will definitely play a role in shaping our product in the future. Some of the highlights of this year’s exhibit were our newly added features and enhancements to...

Mars Wrigley Confectionery licenses Persephone

18:39 12 November in General News
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We are pleased to welcome Mars Wrigley Confectionery into the growing community of Persephone users. We are looking forward to a fruitful collaboration that will make the work of Mars’ scientists more comfortable and productive, while allowing the Persephone team to benefit from their experience in order to further improve the software....

Web version: Users can edit the map set tree

17:04 12 September in Web Version
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We thought, the users might want to rearrange the map set tree on the left by adding, removing or relocating the nodes. For example, as long as the current demo instance has a random set of genomes loaded, plant biologists may want to remove the node with Homo sapiens maps or leave just one favorite genome, to clear the view: ...