How syedzainalishah/clippr works
CLIPPR designs synthetic PPR regulators from target RNA: it predicts the PPR-code recognition sequence, produces a host-codon-optimized coding sequence, plans Golden Gate assembly, checks synthesis constraints and optional host off-targets, then exports orderable files and an audit. A second route designs libraries and reports pooled-order and cross-talk information; the documented reusable-kit route recodes and optimizes deposited modules. The graph reflects README capabilities and the supplied excerpts; detailed wiring in unsampled modules is not assumed.
Main entry points: design.py Design One Target · library.py Design Library · assembly.py Assembly Plan · recoding.py Kit Host Recoding
Components 20
Single Design
- Design One Target
src/clippr/design.py - PPR Recognition
src/clippr/ppr.py - Host Codons
src/clippr/codons.py - CDS Recoding
src/clippr/recoding.py
Design Checks
- Ligation Fidelity
src/clippr/overhangs.py - Sequence Constraints
src/clippr/substrates.py - Synthesis QC
src/clippr/qc.py - Host Screening
src/clippr/offtarget.py - Decision Audit
src/clippr/audit.py
Assembly And Export
- Assembly Plan
src/clippr/assembly.py - Junction Choices
src/clippr/junctions.py - Design Files
src/clippr/export.py
Libraries And Kits
- Design Library
src/clippr/library.py - Cross-Talk Analysis
src/clippr/crosstalk.py - Deposited Kit
src/clippr/inventories.py - Kit Host Recoding
src/clippr/recoding.py - Collection Search
src/clippr/library_search.py
Other components
- Researcher
- Kazusa Codon Data
- NCBI Genome Data
Connections 22
- Researcher → Design One Target: provides target
- Design One Target → PPR Recognition: derives recognition
- Design One Target → Host Codons: loads codons
- Design One Target → CDS Recoding: optimizes coding
- Design One Target → Assembly Plan: plans assembly
- Design One Target → Sequence Constraints: checks constraints
- Design One Target → Synthesis QC: checks synthesis
- Design One Target → Host Screening: screens host
- Design One Target → Decision Audit: records decisions
- Design One Target → Design Files: writes files
- Assembly Plan → Junction Choices: selects junctions
- Assembly Plan → Ligation Fidelity: scores fidelity
- Kazusa Codon Data → Host Codons: supplies table
- NCBI Genome Data → Host Screening: supplies genome
- Researcher → Design Library: provides targets
- Design Library → Design One Target: designs members
- Design Library → Cross-Talk Analysis: analyzes set
- Design Library → Design Files: writes pooled files
- Researcher → Deposited Kit: provides kit data
- Deposited Kit → Kit Host Recoding: supplies modules
- Kit Host Recoding → Host Codons: uses host table
- Kit Host Recoding → Collection Search: refines collection