Warning
This package is under active development.
Until the first stable release (v1.0.0), the API may change without notice.
Expect breaking changes in minor releases, and pin your dependency to a specific version if you use it in production.
Genome-scale oligonucleotide probe design for DNA and RNA FISH.
OligoMiner2 is a Python package for designing oligonucleotide probes used in fluorescence in situ hybridization (FISH) experiments. It takes a target genome or transcriptome as input and returns candidate probe sequences that are thermodynamically optimized and filtered for specificity.
- Mine candidate probes from FASTA sequences, filtering by melting temperature, GC content, length, homopolymer runs, and prohibited subsequences.
- Align candidates against a reference genome with Bowtie2 to identify off-target binding sites.
- Score specificity using k-mer frequency analysis (Jellyfish) and thermodynamic duplex stability predictions (NUPACK / XGBoost).
from oligominer import mine_fasta
# mine candidate probes with default parameters
df = mine_fasta('genome.fa')Full documentation including API reference and example notebooks is available at the OligoMiner2 docs site.
OligoMiner2 is open-source software. See LICENSE for details.