Blog

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"...

Search Functionality Improved

22:07 18 March in Web Version
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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
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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).  ...

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....