---
description: Documentation for CRISPR guide RNA design algorithms and sequence analysis logic
globs: **/guide-design.ts,**/sequence-analysis.py,**/dna_sequence.rs,**/off-target-prediction.ts
alwaysApply: false
---


# crispr-algorithms

The CRISPR guide RNA design system implements specialized algorithms for sequence analysis and guide RNA optimization:

## Guide RNA Design Core
**Importance: 95**
File: `/apps/web/src/lib/crispr/guide-design.ts`

- GC content calculation for target sequences
- PAM site identification using pattern matching
- Scoring mechanism for guide RNA efficiency:
  - Position-specific nucleotide weights
  - Secondary structure impact assessment
  - Target accessibility scoring

## Off-Target Analysis
**Importance: 90**
File: `/apps/web/src/lib/crispr/off-target-prediction.ts`

- Implementation of CFD (Cutting Frequency Determination) scoring
- MIT off-target scoring matrix integration
- Mismatch pattern analysis with position-weighted scoring
- Risk assessment categorization based on aggregate scores

## Sequence Validation
**Importance: 85**
File: `/lims-core/src/validation/dna_sequence.rs`

- ATCGN pattern validation for input sequences
- Guide RNA length constraints (20-25 nucleotides)
- Score range enforcement (0-1) for efficiency metrics
- Special handling for degenerate base pairs

## Batch Analysis Pipeline
**Importance: 80**
File: `/apps/web/src/lib/crispr/batch-processing.ts`

- Multi-sequence FASTA format processing
- Parallel guide RNA design for multiple targets
- Results aggregation with comparative scoring
- Optimization suggestions based on batch patterns

$END$

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