We added the Homo sapiens genome version CHM13 from Telomere-to-telomere consortium (https://sites.google.com/ucsc.edu/t2tworkinggroup/). The new data set provides additional sequences missing from the GRCh38 genome project. The authors claim that their technology allowed the addition of 200 Mbp of new sequences. The...
A study on predicting promoters of several conifer species has been published by International Journal of Molecular Sciences (link). The paper called Genome-Wide Prediction of Transcription Start Sites in Conifers references Persephone's web portal used as the repository of the...
The synteny matrix in the desktop version of Persephone that visualizes the alignment of entire genomes has a useful feature - clustering the connectors in the dot plot. Collinear connectors between orthologs or markers appear as a series of dots...
Yet another variant of the notorious SARS-CoV-2 coronavirus, called omicron, have been added to our records. It is available in Persephone at https://web.persephonesoft.com/?data=genomes/OL672836.1. Using the "instant BLAST" feature (push that green button), it is easy to align the genomic sequences...
We continue migrating the features originally implemented in the desktop application to the Web version. This time, we added the Synteny matrix - a dot plot that visualizes full genome comparison. Each dot in the plot represents a connector -...
The gene properties form shown for a selected gene model has now a new tab, called Transcripts: This control displays alternative splice variants with corresponding measurements. A reference isoform (highlighted) is compared to the other variants. Whenever an exon is different...
Our loader application PersephoneShell used to upload the data to the Persephone database provides commands to calculate ortholog gene pairs. By default, we use reciprocal BLASTP as the protein sequence aligner. A much faster alternative to BLASTP called DIAMOND (http://diamondsearch.org)...
We have added the genome of Vigna unguiculata v1.2 (cowbean) with gene annotation to our web version of Persephone. The calculated orthologs between cowbean and soybean genes allow visualizing the synteny intervals between the two genomes. We also downloaded the...
Max Troukhan, Ph.D, is going to present this video talk at BiATA conference. It gives a quick overview of the major features of Persephone for the Web. https://www.youtube.com/watch?v=ie7LFV1Hu_Q ...
The recent COVID-19 pandemic profile is changing, and now it is mostly dominated by the coronavirus strain called delta (B.1.617.2) that caused massive problems in India and other countries. We loaded its genome with the gene annotation to our web...