Product · SELEX analysis pipeline · Waterloo

AptaPilot

From a SELEX pool to a validated shortlist.

Software that helps aptamer researchers test the candidates that actually bind — and skip the dozens that don't.

Try the tools → Talk to us
Analyze→ Fold→ Cluster→ Fit Kd
/ Demo

See it in one pass.

Fig. 00 — Full pipeline demo Self-hosted · ~5 min
/ The problem

Sequencing is cheap. Deciding is not.

A single SELEX experiment produces thousands to millions of candidate sequences. The hard, expensive part isn't sequencing — it's deciding which few to synthesize, truncate, and validate by ITC / CD / FRET.

Today that decision rests on a patchwork of aging, disconnected tools:

  1. 01

    Clustering by full-length sequence similarity splits real binding families apart.

  2. 02

    Structure is predicted with decades-old, monovalent-only tools (mfold / UNAFold) that ignore the Mg²⁺ / K⁺ / Ca²⁺ in real buffers — and miss G-quadruplexes entirely.

  3. 03

    Binding affinity is fit in spreadsheets.

The cost: wasted synthesis and truncation rounds on sequences that never bind, and real binding motifs that get missed.

/ What AptaPilot does

One connected pipeline.

AptaPilot connects the SELEX analysis workflow into one pipeline, so you reach a short, structure-aware shortlist faster.

01

Analyze the pool

Trim, cluster, and report from raw sequencing data.

02

Fold under real conditions

Predict structure with the actual assay buffer (Na⁺ / Mg²⁺ / K⁺ / Ca²⁺ and temperature), including G-quadruplexes.

03

Find the families that matter

Group candidates by loop structure and surface each family's conserved motif — the likely binding core that tells you where to truncate.

04

Fit binding affinity

Get clean Kd curves, ready for figures.

The result: labs spend bench time on the candidates that actually bind.

/ The tools

Four tools, one shortlist.

01 Desktop · Win + macOS

Aptamer Analysis Tool

SELEX FASTQ trimming, family clustering, and PDF / PNG / XLSX / Word reports. Tunable clustering, tiered trim modes, unattended batch runs. Fully local.

View & download → 01 / 04
02 Desktop · Windows

AptaFold

DNA aptamer secondary-structure prediction with explicit Na⁺ / Mg²⁺ / K⁺ / Ca²⁺ and temperature inputs and native G-quadruplex detection and rendering. Built to replace mfold / UNAFold for routine SELEX work.

View & download → 02 / 04
03 Web · No install

Kd Fitting Tool

Quadratic binding-model Kd fitting from concentration / signal data. Paste from Excel, fit, export the curve. Runs entirely in your browser — nothing is uploaded.

View & launch → 03 / 04
04 Experimental

Structural Family Classification

Classifies SELEX aptamers by loop-region structure instead of full-length sequence, so aptamers with the same fold but different stems land in one family. Currently under wet-lab validation.

View → Under validation
/ What makes it different

Structure-first, not string-first.

◈

Folds under your real assay conditions

Divalent cations (Mg²⁺ / Ca²⁺) and G-quadruplexes, not just sodium — the ions your buffers actually contain.

⟁

Structure-first, not string-first

Groups candidates by the architecture that drives binding, and points at the conserved motif — where to truncate.

⇄

One connected pipeline

Each tool reads the previous one's output, instead of a pile of one-off scripts and manual hand-offs.

⌬

Built by practitioners

Developed in an active SELEX lab to solve its own bottlenecks — and in daily use there.

/ Who it's for

Labs that run SELEX.

Downstream, the aptamers these labs discover power diagnostics, biosensors, therapeutics, food-safety testing, and environmental monitoring.

/ Where we are

Working today, calibrating tomorrow.

In active use

The core tools are working and used daily in the lab; some modules (e.g. the structural family classifier and the divalent-cation folding engines) are experimental and under wet-lab calibration. We're currently talking to labs and companies to learn what they need most — if that sounds like you, we'd love to hear from you.

/ Who we are

From the bench, to the market.

The team

AptaPilot is built in Prof. Juewen Liu's lab (Bionanotechnology & Interfaces Laboratory) at the University of Waterloo, led by Dr. Xiaohan Zhang, with a small team spanning software development, commercialization, and customer discovery.

Dr. Xiaohan ZhangEntrepreneurial Lead

Problem, product hypothesis, customer-discovery goals, and the final go / pivot / no-go decision; software & algorithms; main speaker.

Prof. Juewen LiuTechnical Lead & Supervisor

Scientific credibility, why the problem is real now, and the lab + wet-lab grounding behind AptaPilot.

Dr. Ka-Ying WongCommercialization & IP

Commercialization, IP, interview design, and feedback interpretation.

Yuanli LiSoftware Development

Development support; turns customer feedback into product requirements.

Amira KamelCustomer Discovery

Interviews, surveys, and feedback synthesis.

QR code linking to the AptaPilot introduction document on Google Docs
/ Full write-up · Google Doc

Read the complete AptaPilot introduction

Scan the code for the full project document — the problem, the pipeline, the validation plan, and the team, in one place.

QR code to the 4K AptaPilot intro video on YouTube
/ 4K intro video · YouTube

Watch the 4K walkthrough

Scan to watch the full 4K AptaPilot intro on YouTube (best on a fast connection).

/ Contact

Want to try the tools, share what your lab struggles with, or explore working together?

[email protected]
AptaPilot — predict, then validate.