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protein-subcellular-localization-prediction-biot5

Predicts subcellular localization of proteins from FASTA amino acid sequences using BioT5 inference pipeline.

1.1k|132|Updated Apr 13, 2023
Search Tags:#localization#bioinformatics#protein#sequence-analysis#biot5#subcellular
One-click install
npx skills add https://github.com/PharMolix/OpenBioMed --skill protein-subcellular-localization-prediction-biot5
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: protein-subcellular-localization-prediction-biot5
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/protein-subcellular-localization-prediction-biot5
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill protein-subcellular-localization-prediction-biot5

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Protein sequences and annotations often lack localization context; this skill predicts the subcellular compartment from amino acid sequences to accelerate functional interpretation.

Core Features & Use Cases

  • BioT5-based localization predictions from FASTA inputs, classifying cytoplasm, nucleus, membrane, secreted, mitochondria, ER, Golgi, and other compartments.
  • Enables rapid localization-informed prioritization for experiments, annotations, and design of targeting strategies.
  • Use Case: Given a novel protein sequence, obtain a likely localization to guide experimental planning.

Quick Start

Submit a protein amino acid sequence in FASTA format to obtain a predicted subcellular localization.

Frequently Asked Questions about protein-subcellular-localization-prediction-biot5

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

FAQPage Schema
How do I predict protein subcellular localization from an amino acid sequence?▼

To predict protein subcellular localization from an amino acid sequence, submit your input in FASTA format to the BioT5-based inference pipeline, which classifies proteins into compartments like cytoplasm, nucleus, or membrane.

What compartments can be identified using BioT5 for subcellular localization?▼

Subcellular localization using BioT5 identifies compartments including cytoplasm, nucleus, membrane, secreted, mitochondria, ER, Golgi, and other organelles, enabling rapid functional interpretation for protein characterization workflows.

Does this subcellular localization prediction work with FASTA inputs?▼

Yes, subcellular localization prediction works directly with FASTA inputs, requiring an amino acid sequence to classify the protein's likely residing compartment using a BioT5-based inference pipeline.

What is the maximum sequence length for predicting protein localization with BioT5?▼

The maximum sequence length for predicting protein localization with BioT5 is 512 residues, requiring sequences to fit within this limit for accurate subcellular compartment classification.

Can I run protein sequence analysis for localization on a CPU without a GPU device?▼

Yes, you can run protein sequence analysis for localization on a CPU, as the inference pipeline accepts a device specification allowing either cuda:0 for GPU acceleration or cpu for standard processing.

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