What it does
Library Planner takes a parent sequence plus a list of hotspot residues and returns a ranked plan for a combinatorial mutation library suited to yeast surface display. The output covers theoretical diversity against codon scheme (NNK, NNS, NNN, or trimer mix), achievable diversity against the yeast transformation ceiling (typically 1e8 to 1e9 transformants), expression-readiness flags on the parent scaffold, and a primer design ready to drop into a synthesis quote.
Each candidate library is scored for feasibility: whether the requested diversity is actually reachable, whether the sort depth supports the number of rounds you plan to run, whether the scaffold has known expression liabilities in S. cerevisiae, and whether the diversified positions cluster in regions that disrupt Aga2p display.
What it is not
Library Planner is not a cloning wizard or a gene synthesis vendor. It is the step before synthesis: the calculation pass that tells you whether the library you have in mind is physically reachable, informationally sound, and biologically sensible before you spend money on oligos. It also is not specific to antibodies — any scaffold displayed as an Aga2p fusion (scFv, VHH, DARPin, affibody, fibronectin domain, de novo mini-binders) fits the same framework.
Methodology
Diversity math is standard combinatorial: for N diversified positions with an effective alphabet of k per position, theoretical diversity is k to the Nth. NNK contributes a 32-codon alphabet encoding 20 amino acids plus 1 stop (effective k approximately 20.3 when the 5 percent stop frequency is accounted for). Trimer mixes give a full 20 amino acid alphabet per position with zero stop frequency at roughly 3x the synthesis cost. S. cerevisiae codon bias is applied to expression-level predictions.
Sort depth is Poisson-based: given a library of size L and a sort round collecting N cells, the probability that any given variant is sampled at least once is 1 minus the Poisson zero-class at lambda equals N over L. The tool reports this coverage number per round and flags rounds where the sort depth is insufficient to preserve diversity.
Expression-readiness flags come from a lightweight sequence-level check for S. cerevisiae expression blockers: unpaired cysteines outside disulphide-forming positions, N-linked glycosylation sequons at surface positions, and extreme hydrophobicity at the Aga2p linker junction.
When to use it
At the scoping stage of any yeast display campaign. Teams routinely commit to libraries that are either too large (diversity exceeds the transformation ceiling by two orders of magnitude, so most theoretical variants are never sampled) or too small (diversity is well under the sort depth, so sorting does no selection). The planning pass catches both mistakes in seconds rather than after three rounds of wasted sorting.
Also useful for: comparing NNK versus trimer cost and coverage trade-offs, budgeting NGS read depth per round against expected diversity, and documenting a defensible library design for IND-directed campaigns.
Pricing
Free forever, no account required. CSV and PDF export included.
From library plan to validated binders
Library Planner tells you what to build. Building and screening it is the next step, and is exactly what our yeast display platform does. If you want the library designed, synthesised, sorted, and NGS-tracked on a fixed scope, the Binder Pilot is the smallest entry point into that pipeline.