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SpliceTransformer intron boundary score
License: SpliceTransformer is open source and free for academic and commercial use under an Apache-2.0 license. Please refer to the license for full terms.

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evo-design/proto-language/proto_language/constraint/rna_splicing/splice_transformer_intron_boundary.py
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Score donor/acceptor splice sites for three-segment intron boundaries. Accepts three segments (left_flank, intron_core, right_flank), concatenates them into a single 1-kb target sequence, and scores donor/acceptor splice sites.

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API Reference

ConfigSpliceTransformerIntronBoundaryConfig Source
Configuration for SpliceTransformer intron boundary constraint.This class defines configuration parameters for evaluating splice site quality using SpliceTransformer, a deep learning model trained to predict splice sites in pre-mRNA sequences. The constraint assesses whether specified positions in a sequence are likely to function as authentic splice sites, which is critical for proper intron removal and mRNA processing.
SpliceTransformer requires sequences of specific lengths:
  • Concatenated target (left_flank + intron_core + right_flank): scored over a 1000 bp window. If the concatenation is longer, it is windowed to 1000 bp centred on the donor/acceptor positions and the positions are remapped into that window.
  • Left context: Must be exactly 4000 bp
  • Right context: Must be exactly 4000 bp
  • Total sequence analyzed: 9000 bp (4000 + 1000 + 4000)
The model outputs splice site probabilities for each position. Higher scores indicate stronger predicted splice sites. Authentic splice sites typically have scores > 0.5, while non-splice positions have scores near 0.
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string
required
Sequence of the left context for SpliceTransformer
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string
required
Sequence of the right context for SpliceTransformer
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List[integer]
required
0-indexed position(s) into the concatenated target sequence of expected donor
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List[integer]
required
0-indexed position(s) into the concatenated target sequence of expected acceptor
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enum
default:"mean"
Combine donor/acceptor probs: ‘mean’ (average) or ‘min’ (weaker site must be strong).Options: mean, min
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integer
default:"0"
Max donor/acceptor probability within +/- this many positions of the index; 0 = exact index.
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SpliceTransformerConfig
Advanced parameter configuration for SpliceTransformer.
ReturnsConstraintOutput
One result per input. score is the combined boundary penalty in [0.0, 1.0]. metadata carries donor_pos, acceptor_pos, donor_score, acceptor_score, and total_splice_score.

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Usage

python

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Metadata