Our collection of genomes at the web portal has three new additions: Coffea arabica, Coffea eugenioides, and Coffea humblotiana. All three genomes can be aligned to each other using the gene ortholog pairs. As usual, this reveals the synteny and...
With our colleagues from KAUST and other organizations, we are preparing the new publication on the analysis of 18 reference genomes from the "Rice Platinum Standard". The pre-print has been submitted to bioRxiv (Pan-genome inversion index reveals evolutionary insights into...
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...