oligoN-design

oligoN-design designs specific oligonucleotide probes and primers from large heterogeneous datasets for ecological and evolutionary studies relying on PCR or FISH.

Key Features:

• Target-specific oligonucleotide design: Designs oligonucleotides specific to a set of target sequences while minimizing predicted binding to non-target sequences.
• Minimal input requirements: Requires only two fasta files as input, one containing target taxa and the other containing non-target taxa.
• Integration with standard bioinformatic tools: Uses standard bioinformatic formats and integrates easily with BLAST, VSEARCH or MAFFT.
• Flexible usage strategies: Supports a range of strategies from unsupervised end-to-end usage to detailed expert usage.
• Performance on large datasets: Replicates known taxa-specific oligonucleotides from large comprehensive ribosomal databases (PR2, SILVA) in under 30 minutes using up to 6 Gb of RAM.

Scientific Applications:

• PCR primer design: Designs taxon-specific primers for Polymerase Chain Reactions from high-throughput environmental DNA sequencing data.
• FISH probe design: Designs specific probes for Fluorescence in situ Hybridization applications.
• High-throughput sequencing data analysis: Addresses the bottleneck of designing taxon-specific oligonucleotides from thousands to millions of DNA sequences in molecular environmental datasets.

Methodology:

The tool accepts two fasta files as input and uses standard bioinformatic formats for integration with BLAST, VSEARCH or MAFFT.