Desktop Version

Windows version: Tomato Genome SL3.0 Added

21:43 14 May in Desktop Version
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The genome sequences and gene annotation of Solanum lycopersicum (tomato SL3.0) have been loaded from Phytozome v.13. We added NCBI's Gnomon gene models too, for comparison. Sequences of a close relative, potato, can be aligned to the tomato chromosomes by linking the orthologous genes: [caption id="attachment_15093" align="alignleft" width="867"] Example of potato-tomato synteny. Chromosome 1 from tomato (left) is aligned vs. chromosome 1 from potato (right). See it yourself[/caption]...

Desktop Version: Sequence Is Shown for Entire Chromosomes

17:57 30 April in Desktop Version
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We have added a new track to the vertical view of maps - a GC-content track, previously shown in the horizontal view only. The most useful utility of this track is the ability to show poly-N spacers, drawn in blue. A quick look at a chromosome map would reveal the regions with unfinished or masked sequences, quickly showing the status of sequencing for a particular genome. Aligning several maps may illustrate the history of sequence refinement: [caption id="attachment_15082" align="alignleft" width="538"] The entire Sorghum bicolor genome is shown. The blue bars are marking the poly-N spacers, mostly located in centromeric regions[/caption] [caption id="attachment_15081"...

ClinVar Track Added

20:14 15 April in Desktop Version, Web Version
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ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. We have created a track with 441,959 markers corresponding to the ClinVar entries. Each marker has multiple qualifiers including the ones that describe the medical consequences of a mutation, allele frequencies, etc. Note, some of the marker positions correspond to mapping locations of the probes from Illumina OmniExpress24 array, for which we also have the assay sequences loaded. The RS identifier will help locating the corresponding probe. The new track will appear in both the Web and the Windows versions.  ...

New BLAST Interface Allows Selecting Individual Maps

21:20 21 March in Desktop Version
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If you have worked with the wheat or human genome, you are probably familiar with a typical long wait for getting BLAST search results for these quite large genomes. To save you some time, we have introduced a feature in Persephone Windows version that allows selecting individual maps for BLAST search. (By the way, the web version has had it for quite some time). In case the set of maps contains a mixture of chromosomes and multiple scaffolds, the user will still be able to select individual chromosomes. To select the rest of maps, most probably scaffolds, we added a node called "Other"...

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)...

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....