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intronIC (intron Interrogator and Classifier)

Version 3.1.0: a cross-species U12-type/U2-type classifier built from a raw-feature RBF-SVM motif ensemble plus a single output-level species adjudicator

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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Features

• Raw-feature RBF SVM motif ensemble: a single calibrated ensemble (42 sub-models / 210 sub-estimators; RBF C=200, γ=0.001, isotonic) scores each intron's background-corrected raw 5′SS / branch-point / 3′SS motif log-odds plus branch-point geometry, yielding P_motif: a species-agnostic, Platt-calibrated U12-type motif probability (0–1). No per-species z-normalization.
• Output-level species adjudicator: all per-species adaptation lives in one post-scoring layer. A per-species z_excess count statistic (plus a per-genome strength gate) assigns each genome a motif_category ∈ {DETECTED, INCONCLUSIVE, NOT_DETECTED, UNASSESSABLE}. Only NOT_DETECTED suppresses calls.
• Species-specific background correction: corrects the U2-type PWMs against the target genome's own nucleotide composition so raw motif log-odds stay comparable across eukaryotic diversity (on by default; see Technical Details)
• Pretrained model for cross-species analysis, with no per-species retraining or recalibration required
• Streaming mode keeps peak memory roughly half of in-memory mode, with results identical to in-memory (see Memory and performance)
• Parallel processing (-p)
• YAML configuration for reproducible analysis pipelines
• Per-intron metadata: phase, position, parent gene/transcript

Quick Links

Quick Start: Installation and first run Overview: Algorithm and classification basics Output Files: Understanding results Full Usage Info: Complete CLI reference

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Documentation

• Overview — Classification approach and basic usage
• Quick start — Installation and testing
• Technical Details — Algorithm and data flow
• Data filtering notes — Filtering criteria and tags
• Output files — File formats and columns
• Training data and PWMs — Reference data and matrices
• Example usage — Common use cases
• Full usage info — Complete argument reference
• About — Background and motivation

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Citation

If you use intronIC in your research, please cite:

Moyer DC, Larue GE, Hershberger CE, Roy SW, Padgett RA. (2020) Comprehensive database and evolutionary dynamics of U12-type introns. Nucleic Acids Research 48(13):7066–7078. doi:10.1093/nar/gkaa464