Bioconductor Seqlogo

Organization

bioMate-AI

bioconductor-seqlogo

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

Overview

Publisher	bioMate-AI
Repository	`biomate-bioconductor-kb`
Skill name	`bioconductor-seqlogo`
Stars	804
Forks	66
Bundled files	Instructions only
Links	Skill source Repository

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by bioMate-AI on GitHub. Read the source before you install it.

Installation

Install the Bioconductor Seqlogo AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/seqlogo
Enable the skill in any chat where you want it available.

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git /tmp/biomate-bioconductor-kb
mkdir -p .claude/skills
cp -r /tmp/biomate-bioconductor-kb/skills/general/seqlogo .claude/skills/bioconductor-seqlogo

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Bioconductor Seqlogo in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Bioconductor Seqlogo on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Bioconductor Seqlogo is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

seqLogo

When to Use

Visualizing sequence logos for DNA sequence alignments using seqLogo().
Representing position weight matrices (PWM) and their information content profiles using makePWM().
Plotting RNA sequence logos by specifying the RNA alphabet and custom fill colors.

When NOT to Use

For highly customized ggplot2-based sequence logos, use ggseqlogo instead because seqLogo uses the base grid package for rendering.
For protein/amino acid sequence logos, use ggseqlogo instead because seqLogo is currently implemented primarily for DNA/RNA sequences.

Data Requirements

A simple matrix or data.frame where column probabilities add up to 1.0.
An instance of the pwm class created by makePWM().

Key Parameters

pwm: The position weight matrix for which the sequence logo is to be plotted (can be a pwm object, matrix, or data.frame).
ic.scale: Logical indicating whether the height of each column is to be proportional to its information content.
fill: A named character vector to change the default colors for the nucleotides (e.g., A, C, G, T or U).
alphabet: Character string to specify the alphabet, such as "RNA" for RNA logos.

Best Practices

Construct a pwm object from a matrix or data frame using makePWM() to automatically check that column probabilities sum to 1.0.
Use ic.scale=FALSE if you want all columns to have the same uniform height rather than being scaled by information content.
When plotting RNA logos, specify alphabet="RNA" in makePWM() and provide fill colors for either c("A", "C", "G", "U") or c("A", "C", "G", "T").

Common Pitfalls

Unnormalized Matrix: Column probabilities do not sum to 1.0. Fix: Ensure the input matrix or data.frame is properly normalized before passing it to makePWM().
Incorrect color mapping for RNA logos: The default colors may not map correctly to Uracil. Fix: Provide a named character vector to the fill argument in seqLogo() with specific colors for A, C, G, and T/U.
Attempting to plot amino acid sequences: The package will fail or produce incorrect logos. Fix: Use a different package, as the vignette notes seqLogo is designed for DNA/RNA alignments.

Alternatives

ggseqlogo: Uses ggplot2 for rendering, allowing for more modern and flexible plot customization.
universalmotif: Provides comprehensive motif manipulation and visualization for various alphabets.
motifStack: Allows plotting stacked logos and tree-structured logos for multiple motifs.

Citations

Schneider, Thomas D., and R.Michael Stephens. 1990. "Sequence logos: a new way to display consensus sequences." Nucleic Acids Research 18 (20): 6097-6100.
Schneider, Thomas D., Gary D. Stormo, Larry Gold, and Andrzej Ehrenfeucht. 1986. "Information Content of Binding Sites on Nucleotide Sequences." Journal of Molecular Biology 188 (3): 415-31.

References

Homepage: https://bioconductor.org/packages/seqLogo
Vignette: https://bioconductor.org/packages/release/bioc/vignettes/seqLogo/inst/doc/seqLogo.pdf

Run this on BioMate

This skill is the knowledge layer — when, why, and how to use seqlogo. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.

▶ Open seqlogo on BioMate →

Frequently asked questions

What does the Bioconductor Seqlogo AI skill do?

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

Why use Bioconductor Seqlogo on TypingMind?

Because you install it once and use it with any model. Bioconductor Seqlogo is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Bioconductor Seqlogo in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/general/seqlogo. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Bioconductor Seqlogo?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Bioconductor Seqlogo?

As many as you like. As long as a model supports skills, you can use Bioconductor Seqlogo with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Bioconductor Seqlogo AI skill free?

It is published on GitHub by bioMate-AI. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

seqLogo

When to Use

When NOT to Use

Data Requirements

Key Parameters

Best Practices

Common Pitfalls

Alternatives

Citations

References

Run this on BioMate

Frequently asked questions

Related AI Skills

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