Data
Genome browser
Sixty-five organisms, annotated and navigable down to the base. Pathway loci, designed edit sites and construct placements render in the same view, so a design is visible in the context it has to live in.
65
organisms
14.1 Mbp
designed DNA
seqviz
renderer
Free
to browse
01
What the dataset is
Every organism in the catalog arrives with an assembly, a feature set and a layer of project-specific annotation describing where the capsaicinoid pathway sits — natively, in the Capsicum species, or as designed insertions in the sixty-odd hosts that have no pathway of their own. The browser is how you read that layer in place.
Hosts range from the obvious to the deliberately strange. Peppers anchor one end; tomato, tobacco, and a long tail of cross-species hosts occupy the rest, which is where most of the interesting design constraints come from. A pathway that behaves predictably in Capsicum chinense has to be argued for everywhere else.
02
What the view shows
Annotated features
Genes, coding sequences, UTRs, regulatory regions and repeats, rendered by seqviz with Biopython handling the records underneath. Linear and circular views for whichever the sequence calls for.
Pathway loci
PAMT, the pun1 locus and the rest of the capsaicinoid machinery are marked explicitly, including in hosts where the pathway was introduced rather than inherited.
Designed edit sites
Guide target sites from the project appear against the genome with their off-target evidence attached, so a guide's neighbourhood is visible rather than something you have to look up separately.
Construct placements
Where a construct is intended to land, with its parts laid out in order and each part linked back to its record in the builder.
Expression context
Where transcriptomic data exists for a host, tissue-level expression renders alongside the sequence — the difference between a promoter that works and one that works in the tissue you need.
Comparative view
Align a locus across hosts using MAFFT and read the conservation directly. Useful for deciding whether a part that worked in one species has any chance in another.
03
A worked look
- Organism
- Capsicum chinense
- Locus
- pun1 / capsaicin synthase
- Tracks shown
- Features, edits, expression
- Related project
- SS-0188 — Tier 4 habanero line
- Guides in view
- 3, with off-target counts
- Comparative set
- 6 hosts, MAFFT alignment
- Renderer
- seqviz, linear
The pun1 locus is the standard place to start, because it is where the catalog’s heat differences are easiest to read. Pull it up in habanero, turn on the expression track, and the fruit-tissue specificity that makes the pathway useful is visible immediately. Add the comparative alignment and the question of what transfers to another host stops being abstract.
Everything in the view is linked. A guide track entry goes to its off-target sweep; a construct placement goes to the assembly; an annotation goes to the run that produced it. Browsing and designing are the same surface.
04
What you can learn from it
Whether a host has the precursor machinery to make a target plausible. Whether a promoter has the tissue specificity a design assumes. Whether an edit site sits somewhere with a crowded off-target neighbourhood. Whether a part that worked in one species has a conserved counterpart in another, or is about to be an experiment in its own right.
Browsing, annotation and alignment are CPU work and free. Credits only matter when a question turns structural and you move to folding or variant scoring.
Ready to run it
Try this in the Splice Platform.
CPU engines are free to run. GPU engines run on prepaid credits.
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