oligominer 0.0.1.dev1

Python package for genome-scale design of oligo probes for DNA/RNA FISH.

OligoMiner2

[!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.

The pipeline

1. Mine candidate probes from FASTA sequences, filtering by melting temperature, GC content, length, homopolymer runs, and prohibited subsequences.
2. Align candidates against a reference genome with Bowtie2 to identify off-target binding sites.
3. Score specificity using k-mer frequency analysis (Jellyfish) and thermodynamic duplex stability predictions (NUPACK / XGBoost).

Quick start

from oligominer import mine_fasta

# mine candidate probes with default parameters
df = mine_fasta('genome.fa')

Documentation

Full documentation including API reference and example notebooks is available at the OligoMiner2 docs site.

License

OligoMiner2 is open-source software. See LICENSE for details.