Windows version: Tomato Genome SL3.0 Added

21:43 14 May in Desktop Version

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

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

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

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"...

Search Functionality Improved

22:07 18 March in Web Version

We have replaced an older Lucene search engine with a more advanced Apache Solr. We are very pleased with the results of the change: besides much improved response times for fetching the results, the indexing process is now 5 times faster. The search interface has been modified too. The users can now type the query keyword on a consolidated page, which will start the search in different sections of the database, and the results will be shown in separate panels - for marker and the gene annotation tracks separately. A more detailed search can be done in the individual tabs which will take into...