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Operator Site Occlusion

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Source
evo-design/proto-language/proto_language/constraint/sequence_annotation/operator_site_constraint.py
View source
Constraint contributors
Score whether a promoter carries an occluding inverted-repeat operator. Each sequence is anchored to its best consensus -35/-10 promoter, the -35 box, -10 box, and a downstream TSS window are taken as occlusion targets, and the sequence is scanned for inverted-repeat operators (two half-sites of length
= min_half_site separated by a gap <= max_gap whose first half-site matches the reverse complement of the second within max_mismatch mismatches). The best operator that overlaps a target by >= min_overlap bp determines the score.

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API Reference

ConfigOperatorSiteConfig Source
Configuration for the repressor-operator presence constraint.Locates the -35 / -10 boxes by best consensus match, defines a TSS window just downstream of the -10 box, then scans for inverted-repeat operators (two half-sites separated by a short gap whose first half-site matches the reverse complement of the second) and checks whether any occludes a promoter element. Lower score = an occluding operator is present.
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integer
default:"7"
Minimum half-site length (bp) for an inverted-repeat operator candidate.
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integer
default:"1"
Maximum gap (bp) between the two operator half-sites.
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integer
default:"1"
Max Hamming mismatches between half-site 1 and reverse complement of half-site 2.
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integer
default:"3"
Minimum overlap (bp) between an operator and a -35/-10/TSS element to occlude it.
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string
default:"TTGACA"
Consensus -35 box (6 bp) used to anchor the promoter.
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string
default:"TATAAT"
Consensus -10 box (6 bp) used to anchor the promoter.
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integer
default:"14"
Minimum -35/-10 spacer (bp) considered when anchoring the promoter.
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integer
default:"20"
Maximum -35/-10 spacer (bp) considered when anchoring the promoter.
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integer
default:"6"
Width (bp) of the TSS window placed just downstream of the -10 box.
ReturnsConstraintOutput
One result per sequence. score is 0.0 when an occluding operator (mismatch <= max_mismatch) is present and rises toward 1.0 as the best occluding candidate drifts away from a valid operator (always >= 0.5 when no valid operator occludes a target, so threshold=0.5 acts as a presence filter). metadata carries an operator dict with the located boxes and best-operator details (None when no candidate can occlude a target).

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Usage

python

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Metadata