PICKY: An Optimal Oligonucleotide Design and Analysis Tool
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Dario Valenzuela
Senior Commercialization Manager, Life Sciences
Web Published:
Iowa State University researchers have developed a software tool that makes designing oligo probes for microarrays, or gene chips, easier, faster and with the highest quality. It also analyzes existing probes to detect potential cross-hybridization sites for trouble shooting, data analysis improvement or discovery

Development Stage:
PICKY version 2.20 has been released, and Macintosh, Unix and PC versions are all available (except the Mac 64-bit version, which will be released later).  Free versions and tutorials are available for download.

DNA microarrays have enabled detailed studies on gene expression, and are used in drug discovery research, comparative genomics, high throughput screening, diagnostics, and other applications.  However, the design of microarrays is crucial for maximizing experimental results.  To facilitate the design of oligonucleotide (oligos) probes used in microarrays, an ISU researcher has developed PICKY, a software tool for selecting optimal oligos.  PICKY allows the rapid and efficient determination of gene-specific oligos based on a given gene set, and can be used for large, complex genomes, such as human, rice or maize. PICKY can also be used to analyze existing microarray probes and evaluate their design quality. Because PICKY uses rigorous whole genome-based thermodynamic screening to identify hydrogen binding sites, it can be utilized for siRNA (short interference RNA) design for gene knockout applications and for discovery of natural miRNA (microRNA) targets. Non-exclusive free licenses are available for the 32-bit version of PICKY; the 64-bit version of PICKY, which allows bigger gene sets to be analyzed, is freely available to nonprofit users using it for non-commercial purposes, but commercial users will need to pay a licensing fee to license 64-bit version of PICKY for commercial use.

This technology is related to ISURF 4280: High-number Gene Fragment Assembly

• Rapid (gene probes sets can be designed in only minutes or hours compared to other design tools that take days or weeks for some large genomes)
• Accurate (PICKY considers thermodynamics when selecting oligos, not just sequence similarity) 
• Versatile (may be used to design arrays and siRNAs or to analyze the quality of existing arrays)
• Independent (as a stand-alone program that works on all major computing platforms; PICKY does not require any third party software program to operate)
Microarray design; oligonucleotide probe and primer design; existing microarray re-analysis; siRNA Design

Patent Information:
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Intellectual Property:
Copyrighted Material - Software

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