What is DNAnalyzer AGENTS.md?

Repository instructions for DNAnalyzer, a Java and Spring Boot application with a command-line tool, a REST API, a web dashboard, and an optional Python DNA-alignment module.

Use them when developing or verifying the Java application, REST endpoints, static dashboard, Docker setup, or Python analysis module.

They point agents to the authoritative architecture, repository map, API, and testing guidance before code is changed.

How VerisimilitudeX/DNAnalyzer configures Codex and OpenCode

Reuse

Borrowing it

Nothing to install: this file belongs to VerisimilitudeX/DNAnalyzer. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/VerisimilitudeX/DNAnalyzer/main/AGENTS.md

Clone the repo

git clone --depth 1 https://github.com/VerisimilitudeX/DNAnalyzer

Made for: Codex, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/verisimilitudex/dnanalyzer/agents-md/github.svg)](https://agentmods.dev/instructions/verisimilitudex/dnanalyzer/agents-md)

Your own site

<a href="https://agentmods.dev/instructions/verisimilitudex/dnanalyzer/agents-md"><img src="https://agentmods.dev/badge/instructions/verisimilitudex/dnanalyzer/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/verisimilitudex/dnanalyzer/agents-md"><img src="https://agentmods.dev/badge/instructions/verisimilitudex/dnanalyzer/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 1,306 This file is loaded in full into every session.

When invoked 1,306 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.01306	$0.01306
Opus 5.5	$0.00522	$0.00522
Sonnet 5.5	$0.00261	$0.00261
Haiku 4.5	$0.00131	$0.00131

Measured 2mo ago against content hash 368de3803fff, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

DNAnalyzer AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

AGENTS.md · 113 lines

How it starts

The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Agent Guide

This file is the entry point for agentic AI and automation tools. It tells an agent what the repository is, where things live, and how to make changes safely. Keep it short. Link out for detail.

What this repository is

DNAnalyzer is a Java 17 + Spring Boot 2.7 application with a static-HTML web dashboard and an optional Python Smith-Waterman module. It ships two interfaces on the same analysis core:

CLI: DNAnalyzer.Main in src/main/java/DNAnalyzer/.
REST API: DNAnalyzer.api.ApiApplication, mounted under /api/v1.

The org.openjfx.javafxplugin is still declared in build.gradle from an earlier GUI experiment, but no JavaFX source code is present.

The static frontend lives in web/. It is served by Nginx in the Docker stack and proxies /api/* to the Spring Boot container.

Canonical references for agents

Read these in order when you are new to the repo:

README.md for the user-facing overview.
docs/ARCHITECTURE.md for the system diagram and component responsibilities.
docs/REPOSITORY_MAP.md for a directory-by- directory index.
docs/API_REFERENCE.md for REST and CLI surface.
docs/development/testing.md for how to run and extend tests.

If an agent makes changes that would invalidate any of the above, update that doc in the same change.

Build and verify

Always run the verification pipeline after a code change:

./gradlew test                     # Unit + integration tests (22 as of 2026-04)
./gradlew build -x test            # Produces build/libs/DNAnalyzer-<ver>-boot.jar
                                   # and DNAnalyzer-<ver>-plain.jar
docker compose config --quiet      # Validates docker-compose.yml

The bootJar has Start-Class: DNAnalyzer.api.ApiApplication. The plain jar has Main-Class: DNAnalyzer.Main (CLI). Do not confuse them.

Conventions that agents frequently get wrong

Read the full file on GitHub · 113 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 113 lines · 1,306 tokens per session scan A 368de3803fff

Subscribe to this mod's changes

DNAnalyzer AGENTS.md is an instructions file published in the GitHub repository VerisimilitudeX/DNAnalyzer (185 stars, last pushed 11d ago), licensed MIT. It adds 1,306 tokens to every session, about $0.0052 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

artificial-intelligence bioinformatics dna-sequencing genomics machine-learning regulatory-elements

DNAnalyzer AGENTS.md next to 6 instructions from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
DNAnalyzer AGENTS.mdVerisimilitudeX/DNAnalyzer	Instructions file	185	11d ago	MIT	A	1,306	Codex, OpenCode
vscode buildNext.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	9,719	GitHub Copilot
next.js AGENTS.mdvercel/next.js	Instructions file	143k	today	MIT	A	7,461	Codex, OpenCode
langchain AGENTS.mdlangchain-ai/langchain	Instructions file	149k	yesterday	MIT	A	4,680	Codex, OpenCode
vscode oss-third-party-notices.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	5,516	GitHub Copilot
vscode copilot-instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	3,093	GitHub Copilot
deepseek-harness AGENTS.mddeepseek-ai/deepseek-harness	Instructions file	274k	2d ago	MIT	A	4,313	Codex, OpenCode

DNAnalyzer: Instructions file for Codex