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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
52 lines
2.2 KiB
Markdown
52 lines
2.2 KiB
Markdown
# Microsatellite Detection Module (`obimicrosat`)
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This Go package provides tools for identifying and annotating microsatellite (simple sequence repeat, SSR) regions within biological sequences.
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## Core Functionality
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- **`MakeMicrosatWorker(...)`**
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Returns a `SeqWorker` that scans DNA sequences for microsatellite patterns matching user-defined constraints:
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- Minimum/maximum unit length (`minUnitLength`, `maxUnitLength`)
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- Minimum number of repeats (`minUnits`)
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- Overall minimum microsatellite length (`minLength`)
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- Minimum required flanking sequences on each side (`minflankLength`)
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- Optional reverse-complement reorientation flag (`reoriented`)
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## Detection Algorithm
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1. **Initial Pattern Matching**
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Uses a regex of the form `([acgt]{m,n})\1{k,}` to find candidate repeats (where *m*, *n* = unit bounds; *k+1* ≥ `minUnits`).
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2. **Unit Length Refinement**
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Computes the minimal repeating unit via string rotation symmetry detection (`min_unit`).
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3. **Strict Re-Scan**
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Builds a refined regex using the exact unit length to ensure precise boundary detection.
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4. **Flank Validation**
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Ensures sufficient left/right flanking sequences (length ≥ `minflankLength`).
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5. **Normalization & Orientation**
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- Computes the lexicographically smallest rotation (and its reverse complement) to define a canonical unit.
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- Records orientation (`direct`/`reverse`) and, if `reoriented=true`, converts the sequence to its reverse complement.
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## Output Annotations
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Each detected microsatellite adds metadata attributes:
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- `microsat_unit_length`, `microsat_unit_count`
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- `seq_length`, `microsat` (full repeat region)
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- Start/end positions (`microsat_from`, `microsat_to`)
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- Canonical unit: `microsat_unit_normalized`
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- Orientation flag and flanks (`microsat_left`, `microsat_right`)
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## CLI Integration
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- **`CLIAnnotateMicrosat(...)`**
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Wraps the worker in a pipeline stage, applying it to an iterator of sequences.
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- Uses CLI-configurable parameters (e.g., `CLIMinUnitLength()`) and supports parallel processing.
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- Filters out sequences with no qualifying microsatellite matches.
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## Dependencies
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Leverages `obitools4` core types (`BioSequence`, iterators, default attributes) and the `regexp2` library for robust regex matching.
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