Web Version

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.  ...

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...

Illumina’s OmniExpress24 SNP markers have been mapped onto human GRCh38 genome

12:01 07 March in Web Version

We mapped ~ 700K marker sequences from Illumina's OmniExpress 24 v.1.3 onto the latest version of human genome GRCh38 and created a track (highlighted below). The marker sequences used for mapping are stored with the markers and can be visualized in the "Sequences" tab. (To make the reading of marker names easier, we placed the map vertically).  ...

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

17:22 04 March in Web Version

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

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...

Web version: Users can edit the map set tree

17:04 12 September in Web Version

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: ...

Wheat RH Genetic Maps Have Been Loaded

12:14 24 July in Web Version

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

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....

A Free Version of Persephone for Web

15:19 27 November in General News, Web Version

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]  ...