format-conversion

Convert biological sequence files between FASTA, GenBank, and EMBL formats.

6|2|Updated Jun 11, 2026

Search Tags:#bioinformatics #genomics #biopython #sequence conversion #sequence annotation

Ready to run

npx skills add https://github.com/pradyumnasagar/open-research-skills --skill format-conversion

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: format-conversion
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/bioinformatics-sequence/format-conversion
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill format-conversion

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, seqkit, and includes scripts (resource) components.

What problem does it solve?

This Skill streamlines the conversion of biological sequence and annotation formats, allowing researchers to quickly transition between formats like FASTA, GenBank, and EMBL, facilitating tool usage and data sharing.

Core Features & Use Cases

Cross-Format Conversion: Converts between various biological sequence and annotation formats using Biopython.
Batch Conversion: Automates conversion tasks for multiple files.
Lossy and Lossless Conversions: Handles both lossy and round-trip-safe conversions, ensuring data integrity.
Use Case: Researchers needing to convert their genomic sequences from FASTA to GenBank format for submission to a database.

Quick Start

Run the 'format-conversion' skill with the 'from' and 'to' arguments specifying the input and output file formats, e.g., format-conversion from input.fasta to output.gb.

Frequently Asked Questions about format-conversion

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I convert a FASTA file to GenBank format for database submission?▼

To convert a FASTA file to GenBank format, you can use Biopython to automate the sequence format conversion, specifying the input FASTA and output GenBank file arguments to generate a submission-ready file.

Can I batch convert multiple biological sequence files at once?▼

Yes, batch conversion of multiple biological sequence files is supported. The Skill automates conversion tasks for multiple files simultaneously, streamlining transitions between formats like FASTA, GenBank, and EMBL.

Does Biopython support lossless round-trip conversion between FASTA and EMBL?▼

Biopython supports both lossy and round-trip-safe lossless conversions between biological sequence formats, ensuring data integrity is maintained when transitioning between FASTA, GenBank, and EMBL files.

What is the best way to handle sequence annotation conversion for bioinformatics data sharing?▼

The best way to handle sequence annotation conversion is using Biopython to automate cross-format conversions between biological sequence formats, facilitating analysis tool usage and interformat file sharing.

Do I need biopython and seqkit installed to convert genomic sequence formats?▼

Yes, you need both biopython and seqkit installed as dependencies to run the sequence format conversion, which automates transitions between FASTA, GenBank, and EMBL formats for genomic data handling.