Osprey: Oligonucleotide Design Software

Osprey calculates optimal oligonucleotides for a range of tasks: sequence assembly (both contig walking and polishing, with Staden assembly augmented functionality), differential expression, and microarrays (cDNA and spotted oligos). Osprey implements the thermodynamics model proposed by SantaLucia, producing very similar results to HyTher™.

• Extremely sensitive secondary binding checks using Gribskov profiles
• Specification and reporting of secondary binding in terms of melting temperature margins
• Automated optimal length/melting temperature/self-folding energy calculations based on nucleotide composition
• Automated repeats filtering or discrimination

Please cite:

Gordon, P.M.K., Sensen, C.W. (2004) "Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays" Nucleic Acids Research 32(17):e133. PubMed

A commercial licensing scheme for Osprey is currently under development, please restrict your use of Osprey to academic purposes.

Use Osprey to design oligonucleotide microarrays.
Use Osprey to design negative control probes.
Use Osprey to design PCR primers.
Use Osprey to report melting temperature and other stats for given oligonucleotides.