JBrowse 2 integration

An alignment opened in the standalone viewer stands on its own: the columns are the coordinate system, and nothing outside the file has a position in it. The JBrowse 2 plugin opens the same alignment and tree inside JBrowse, beside a genome view, and with protein3d beside an AlphaFold structure as well. Selecting a region in any one of those views highlights the matching columns, codons and residues in the others, so a base in the genome, a column in the alignment and a residue in the fold are the same place.

Each session below is one declarative URL: the link carries the views, the tracks and the data locations, so it opens the state it describes with nothing saved on a server. The tutorials build the alignment and tree files these sessions load.

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, and the highlighted column links the genome to the alignment — Genome ↔ alignment in one JBrowse session: the F12 locus (RefSeq annotation, top) over the react-msaview DNA alignment + species tree, zoomed to base resolution at exon 3. The highlighted column links the genome to the alignment. The four cetaceans carry a single-base deletion (a gap where every other mammal has a C) that disables the gene. The 14-exon model is registered to the alignment columns and lifted onto each species. 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 — Genome ↔ alignment ↔ 3D structure: the TP53 gene (RefSeq + ClinVar), the p53 ortholog alignment, and the AlphaFold structure as one connected session. It opens with the nuclear export signal motif (residues 339–350) highlighted on the genome, the alignment columns, and the folded structure. 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.