Annealed DNA motif optimization
Reproducible fixed-length DNA design for multi-motif regulatory sequences using Gibbs annealing and explicit scoring contracts.
- DNA motif optimization
- Gibbs annealing
- Transcription factor PWMs
- Reproducible run artifacts
cruncher
designs fixed-length regulatory DNA sequences for cases where one short
construct needs to balance several transcription-factor motifs at once. It uses
Gibbs annealing to sample sequence space, keeps motif inputs and scoring rules
explicit, and exports candidate tables, reports, and plots. The trajectory below
comes from
the project_tfs_lexa_cpxr_baer_rcda_lrp_fur_fnr_acrr_soxr_soxs workspace and
shows how candidates move through the optimization process.
Work is ongoing, with additional examples, scoring diagnostics, and implementation notes to follow.