Aptamer Analysis Tool

/ Introduction

What it does.

• Fast EPS recalculation

  After matrix preparation, changing the EPS clustering radius takes seconds instead of the ~10 minutes a full pipeline rerun used to need — making parameter sweeps practical.

• Memory & thread optimization

  Sequence loading, distance calculation, and background scheduling were rebuilt to lower peak memory and stabilize multi-thread runs, so the tool fits more ordinary lab computers.

• Tiered trim modes

  Simple, Pro, and Ultra — from strict standardized trim to fully custom forward/reverse primer regions with adjustable mutation tolerance.

• Multi-file batch processing

  Queue multiple FASTQ files with shared parameters and let the tool run unattended. Failed files are recorded but do not stop the batch.

• Real sequence-context reporting

  PDF / PNG output replaces the old fixed placeholder (e.g. GACGAC---GTCGTC) with the real six bases observed upstream and downstream of the target region, making boundaries easier to validate.

• Local-first, no telemetry

  Normal operation makes zero network calls. Inputs, outputs, and logs all live on your machine; nothing is uploaded.

/ Usage

How to use it.

1. 01

   Launch & pick a workflow

   Open Aptamer Analysis Tool from the Start menu or desktop shortcut. After the splash screen, the main menu offers four workflows: Single File Mode, Batch / Multi-File Mode, Manual / Paste Sequences, and Motif Search. Pick Single File Mode.

   

   Screenshot · 01-main-menu.png

2. 02

   Choose a sequencing file

   Click Choose File and pick a .fastq / .fq / .fastq.gz / .fq.gz file. The tool decompresses .gz automatically and previews the first 5 FASTQ records along with file name and size. Click Next to continue.

   

   Screenshot · 02-choose-file.png

3. 03

   Set trim parameters

   Pick a trim mode. Simple uses fixed flanks GGGACGAC + GTCGTCCCG with strict matching. Pro (A/B/C/D) lets you set Minimum and Maximum target-region lengths and adjust front/rear mutation tolerances (typical defaults: C=0, D=3). Ultra accepts fully custom forward and reverse primer-binding regions for non-standard libraries.

   

   Screenshot · 03-trim-params.png

4. 04

   Prepare matrix

   Click Prepare Matrix. This is the slow part: reading the file, trimming reads, computing the distance matrix, and building clustering coordinates. Large files take longer. You can Cancel at any time; wait for the interface to return to Ready before starting again.

   

   Screenshot · 04-prepare-matrix.png

5. 05

   Set EPS & generate output

   On the output page, enter one or more EPS values (e.g. 0.80, 1.25, 1.50; supported range 0.20–2.20), choose the output folder, and pick formats: PDF / PNG / XLSX / Word. Lower EPS is stricter and emphasizes conserved bases; higher EPS is more permissive. Click Generate Output.

   

   Screenshot · 05-output-page.png

6. 06

   Review & re-run with new EPS

   On the result page, click Open Folder to inspect outputs (named like sample-EPS08.pdf, sample-EPS125.xlsx) or Export to save a run summary. Since the matrix is already prepared, you can return to the output page and re-run Generate Output with different EPS values in seconds.

   

   Screenshot · 06-result-page.png

/ Disclaimer

Things to know.

1. Normal operation is fully offline.

   Aptamer Analysis Tool makes no network calls during normal operation: no telemetry, no automatic update check, no automatic upload. Input file content, file names, output content, and logs never leave your machine.

2. Pro Max activation sends only the minimum.

   The Pro Max build contacts the activation service only when the user requests an activation code by email. The request includes first/last name, the education email entered, application name and version, and a salted hash of the local machine code. Raw hardware serial numbers, file names, file content, logs, and analysis results are not transmitted.

   The code email can take 2–3 minutes to arrive. If it doesn't show up, it's most likely in your spam / junk folder.

3. Logs and crash reports stay local.

   Logs live at %LOCALAPPDATA%\AptamerAnalysisTool\logs on Windows and ~/.pattern_tool/logs on macOS / Linux. Crash files are saved alongside them. They are never sent automatically — sharing one always requires an explicit action by you.

4. Free for academic / non-commercial use.

   Aptamer Analysis Tool is free for academic research and teaching. For commercial integration or redistribution, contact the author in advance.

5. Provided as-is, without warranty.

   Output is best-effort. The author is not responsible for downstream experimental decisions made on the basis of this tool's results. Validate critical findings with independent methods, and report bugs to [email protected].

6. Cite if used in publications.

   If this tool contributed to a published study, please cite: Zhang X. Aptamer Analysis Tool, v0.8, Liu Lab, University of Waterloo, 2026. aptapilot.com/tools/aptamer-analysis.

/ Acknowledgments

Built with the lab.

• 

  Prof. Juewen Liu

  Advisor

  Professor of Chemistry at the University of Waterloo, College member of the Royal Society of Canada (RSC), and Tier 1 Canada Research Chair in Biosensors & Bionanotechnology. Group lead for the aptamer / DNAzyme / nanomaterial research that motivates this tool.

• 

  Boya Zhao

  Initial Python prototype

  Undergraduate at Tsinghua University (Prof. Sichun Zhang's group). Wrote the initial Python script during a research visit to Liu Lab in July 2025 — the prototype that became the algorithmic foundation of the current desktop tool.

• 

  Xiaohan Zhang

  Author · Postdoctoral Researcher

  Postdoctoral researcher at the University of Waterloo under Prof. Juewen Liu. PhD in Inorganic Chemistry, Shandong University (2024). Designed, implemented, and maintains the Windows build.

• 

  Yuanli Li

  macOS port · Beta testing & feedback

  Third-year undergraduate in the Materials Nanoscience joint program (Beijing Jiaotong University × University of Waterloo). Responsible for the macOS adaptation and release, plus extensive beta testing and bug reporting throughout the 0.7.x cycle.

• PySide6
• HDBSCAN
• scikit-learn
• UMAP-learn
• ViennaRNA
• matplotlib
• NumPy
• regex
• requests
• tqdm
• cryptography

/ FAQ

Questions people actually ask.

1. What input files does it accept?

   It reads .fastq, .fq, .fastq.gz and .fq.gz directly — no need to decompress large sequencing archives before analysis.

2. What does the analysis pipeline actually do?

   Sequence trimming, then preparation of a clustering matrix, then EPS-based clustering, then generation of structured reports. Trim configuration is adjustable rather than fixed, so the same build handles libraries with different primer and scaffold layouts.

3. What formats are the reports in?

   PDF, PNG, XLSX and Word — chosen so results can go straight into a lab notebook, a slide deck, or a manuscript supplement without reformatting.

4. Can it handle large batches and long-running jobs?

   Yes — this build was rebuilt over the original Python workflow specifically for interactive performance, lower memory usage and batch processing, with long sequencing batches as the target case.

5. Which platforms, and what does it cost?

   Windows through the AptaPilot Launcher, which installs and updates it for you; macOS as a direct .dmg download while the macOS Launcher is still in progress. Free for academic use.

/ Citation

How to cite.

If this tool contributed to work you are publishing, a citation is the most useful thing you can send back — it is what keeps the tool maintained and lets other people find it.

@software{zhang_aptamer_analysis_2026,
  author  = {Zhang, Xiaohan},
  title   = {Aptamer Analysis Tool},
  year    = {2026},
  version = {0.8},
  url     = {https://aptapilot.com/tools/aptamer-analysis/}
}

/ Also in the toolkit

Other tools.

Web · Online

K_d Fitting Tool

Uses the full binding equation to fit true K_d curves. Data stays in your browser.

Desktop · Windows · Single-file

AptaFold

DNA aptamer folding with Na⁺ / Mg²⁺ / K⁺ / Ca²⁺ / temperature inputs and G-quadruplex detection. Reads this tool's output directly as a batch source.

Desktop · Windows · Experimental

Structural Family Classification

Group SELEX aptamers by loop-region structure with a self-written motif-block classifier. Ingests this tool's trimmed output.