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30 lines
1.5 KiB
Markdown
30 lines
1.5 KiB
Markdown
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# `LocatePattern` Functionality Overview
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The `obialign.LocatePattern` function implements a **local alignment algorithm** to find the best approximate match of a short DNA pattern (e.g., primer) within a longer biological sequence, using **dynamic programming**.
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- **Input**:
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- `id`: identifier for logging/error reporting.
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- `pattern []byte`: the query sequence (e.g., primer).
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- `sequence []byte`: the target read/contig.
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- **Constraints**:
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- Pattern must be strictly shorter than the sequence (`len(pattern) < len(sequence)`).
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- **Scoring Scheme**:
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- Match: `+0` (using IUPAC compatibility via `obiseq.SameIUPACNuc`).
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- Mismatch/Gap: `-1`.
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- **Algorithm Features**:
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- End-gap free alignment (no penalty for gaps at sequence ends), enabling flexible primer positioning.
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- Uses a flattened buffer (`buffIndex`) for memory-efficient matrix storage (width × height).
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- Tracks alignment path via `path` array: diagonal (`0`, match/mismatch), up (`+1`, deletion in pattern/left gap), left (`-1`, insertion/deletion).
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- Backtracks from the bottom-right to find optimal local alignment start/end coordinates.
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- **Output**:
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- `start`: starting index in `sequence`.
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- `end+1`: ending index (exclusive) of best match.
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- Error count: `-score`, i.e., number of mismatches/gaps in alignment.
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- **Use Case**:
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Designed for high-throughput amplicon processing (e.g., primer trimming in metabarcoding pipelines like OBITools4).
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