Variant library
| Document kind | library |
| Drawn from | a file — it can also be previewed in the file manager |
| Formats that open here | Variant library |
| Refuses to draw below | 320px wide |
What it draws
A saturation-mutagenesis library you designed earlier, read back as a document. The design itself happens in the Site-directed mutagenesis tool; this canvas is where a saved design is reopened — weeks later, or by someone else — and read without the session that made it.
The first line answers the two questions a list of positions cannot answer on its own: which protein the positions are numbered in (its name, its length in residues and its strand) and when the library was designed. It then states the design strategy, the library's diversity and how many primer codon sets it needs.
Below that, one row per mutated site:
| Column | What it says |
|---|---|
| Position | the residue number, counted within the protein named above |
| Wild type | the residue there now, with its codon |
| Requested | the amino acids you asked the site to reach |
| Codons | the degenerate codons chosen to reach them (IUPAC, one per primer set) |
| Also encodes | residues those codons produce that you did not ask for, and a stop if any of them can make one |
| Reaches | how many amino acids the site actually covers |
What opens in it
Variant library files (.varlib), which is what Save library in the Site-directed
mutagenesis tool writes into your project. The file is plain, readable JSON, so it can be sent,
diffed and edited by hand; a file that is missing a field is refused with the name of the field,
not half-drawn.
What this computes
Nothing is re-designed here: every number is the one saved with the design, and the view is read-only.
- Diversity — the number of distinct protein variants the library can produce: the product, across sites, of the amino acids each site reaches. It is stored with the design rather than recomputed, so it can be checked against the rows beneath it.
- Over-coverage (Also encodes) — gathered across all the codons chosen for a site, because a degenerate codon encodes what it encodes: asking for A, C and D and receiving a codon that also makes G means the screen will contain G.
- Stop-codon flag — a site whose codons can produce a stop is marked, because that fraction of the library is truncated protein at that position, not a substitution.
Reading it
- A position means nothing without its protein. Residue numbers count from the first residue of the coding sequence named in the header line, and its length excludes the stop codon. Reopen a library only against that protein.
- An en dash in Also encodes is an empty cell, not "none requested". It means the chosen codons reach exactly what was asked for.
- A stop in the design is deliberate, not an error. It appears when the codon set could not cover the requested residues without it, and the note under the table says so.
- Reaches counts residues, not copies. How often each residue appears among a site's codons (and so how many colonies a screen needs) is in the Site-directed mutagenesis tool's Library tab, which draws that composition per site.
Controls
None. It is a record, not a designer: to change the sites, the codon strategy or the requested residues, reopen the design in the Site-directed mutagenesis tool and save it again.
Where it appears
As its own tab on the stage when a saved library is opened, and in the file manager's preview. Both are drawn by the same view, so they cannot disagree.
Performance and limits
A library is a few sites, so there is nothing to thin out. Below 320 px wide the view refuses to draw: the codon column holds a row of degenerate codons, and narrower than that it wraps per codon and the table stops being readable as a table.
Related
- Site-directed mutagenesis: where libraries are designed and saved, and where the per-site composition of a library is drawn.