intronIC 2.2.0

Intron classification tool for identifying U2-type and U12-type introns using SVM

intronIC - (intron Interrogator and Classifier)

intronIC is a bioinformatics tool for extracting and classifying intron sequences as U12-type (minor) or U2-type (major) using a support vector machine trained on position-weight matrix scores.

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Quick Start

Installation

pip install intronIC

Basic Usage

# Classify introns (default model loaded automatically)
intronIC -g genome.fa.gz -a annotation.gff3.gz -n species_name -p 8

# Extract sequences only (no classification)
intronIC extract -g genome.fa.gz -a annotation.gff3.gz -n species_name -p 8

# Train a custom model (optional - most users don't need this)
intronIC train -n my_model -p 8

Test Run

# Quick installation test using bundled test data
intronIC test -p 4

# Or show where test data is located
intronIC test --show-only

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Documentation

• Changelog - Release notes and version history

For complete documentation, see the intronIC Wiki:

• Quick Start Guide - Installation, dependencies, resource usage
• Overview - Classification approach and scientific background
• Usage Info - Complete CLI reference
• Output Files - File formats and interpretation
• Technical Details - Algorithm and ML architecture
• Example Usage - Common workflows
• About - Background and motivation

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What's New in v2.2

• New 8D RBF SVM default model trained on expanded reference data (472 U12 + 30,155 U2 introns)
• Five new classification features: branch point offset, BPS motif sharpness, polypyrimidine tract metrics, and multi-site support scoring
• Reduced false positives: 0 confident false calls in C. elegans (was 2), 1 in Ascaris (was 47)
• See CHANGELOG.md for full release history

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Key Features

• RBF SVM classification with probability scores (0-100%) using 8 sequence-derived features
• Default pretrained model loaded automatically — works for virtually all species
• Streaming mode (default) for ~85% memory reduction on large genomes
• Parallel processing for improved performance (-p 8 recommended)
• Fast runtimes: ~6-10 minutes for human genome with default settings
• Comprehensive metadata including phase, position, parent gene/transcript

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Scientific Background

Most eukaryotic introns (~99.5%) are spliced by the major (U2-type) spliceosome, while a small fraction (~0.5%) are spliced by the minor (U12-type) spliceosome. U12-type introns have:

• Highly conserved TCCTTAAC branch point motif
• Terminal dinucleotides: AT-AC (~25%) or GT-AG (~75%)
• Functional importance and evolutionary conservation

intronIC identifies U12-type introns using:

1. PWM Scoring: Apply position-weight matrices to 5' splice site, branch point, and 3' splice site regions
2. Normalization: Convert raw scores to z-scores via robust scaling
3. Feature Engineering: Compute composite features (multi-site corroboration, BP position, PPT metrics, BPS motif sharpness)
4. SVM Classification: RBF SVM ensemble with balanced class weights outputs probability scores

For detailed algorithm description, see the Technical Details wiki page.

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Citation

If you use intronIC in your research, please cite:

Devlin C Moyer, Graham E Larue, Courtney E Hershberger, Scott W Roy, Richard A Padgett. Comprehensive database and evolutionary dynamics of U12-type introns. Nucleic Acids Research, Volume 48, Issue 13, 27 July 2020, Pages 7066–7078. https://doi.org/10.1093/nar/gkaa464

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Support

• Documentation: intronIC Wiki
• Issues: GitHub Issues
• Discussions: GitHub Discussions

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Contributing

Contributions are welcome! Please see CONTRIBUTING.md for guidelines.

git clone https://github.com/glarue/intronIC.git
cd intronIC
make install    # Set up development environment
make test       # Run tests

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License

intronIC is released under the GNU General Public License v3.0.