JBrowse 2 integration

The JBrowse 2 plugin opens an alignment and tree inside JBrowse, beside a genome view and, with protein3d, an AlphaFold structure. Selecting a region in one view highlights the matching columns, codons and residues in the others.

Each session below is one URL that carries its views, tracks and data locations, with nothing saved on a server.

A single JBrowse session at base resolution over F12 exon 3: the RefSeq gene annotation track on top and the react-msaview DNA alignment with its species tree below. The four cetaceans show a gap where every other mammal has a C, the shared single-base frameshift, in the highlighted column — The F12 locus over its DNA alignment and species tree at exon 3, as two unconnected views. The highlighted column holds the single-base deletion that disables the gene in the four cetaceans. Open in JBrowse ↗

JBrowse: the TP53 gene with ClinVar, the p53 ortholog alignment, and the AlphaFold structure, all connected, with the nuclear export signal motif highlighted across genome, alignment, and 3D structure — The TP53 gene with ClinVar, the p53 ortholog alignment and the AlphaFold structure as one connected session, with the nuclear export signal (residues 339–350) highlighted in all three. Open in JBrowse ↗

Without the structure view

A session with two views instead of three is the same pattern: a gene in the genome view and its family in the alignment, linked by the transcript.

SRC ↗ — the Src-family kinase alignment beside the SRC gene.
BRAF V600E ↗ — the RAF family on the invariant V600 codon, with a ClinVar pathogenic-variant track.
TP53 R248 ↗ — p53 across vertebrates on the R248 hotspot, with ClinVar.

Built when the link opens

The sessions above carry their alignments as files. The two below carry a request instead, and the view builds the alignment when it opens from the translation of the transcript the spec names in connectedTranscript. In these and the gene sessions above, the plugin looks the named transcript's exon model up in the genome view's gene track.

TP53 UniRef cluster ↗ — every reference-proteome protein in UniProtKB within 50% identity of p53, looked up from UniProt and aligned to the transcript in the browser. It submits no job to any service, so it opens in seconds.
TP53 phmmer search ↗ — the same gene through a phmmer search of UniProt's representative proteomes at 15% similarity, the widest net EBI offers: p53's relatives across the tree of life. The wait is EBI's queue, from seconds to many minutes.