Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
PICKY is a whole genome oligo microarray design tool demonstrated in the 2004 PAG microarray workshop. It employs an efficient all-to-all indexing data structure called suffix array to quickly identify all potential cross-hybridization nontargets that might interfere with the correct detection and assessment of the expression level of each targeted gene. It then uses detailed thermodynamic calculations to ensure that all cross-hybridization potentials are eliminated within the design parameters. Since its publication, PICKY has been used by several projects including the NSF Rice Oligonucleotide Array Project.
Ideally each oligo probe on a microarray will measure the expression of a single gene. This can be difficult to achieve given the degree of gene duplication that has occurred in the evolution of many species. There is always a limit beyond which unique oligos cannot be designed for each individual gene no matter how low the design parameters are relaxed. The most notable example is the transposable element related genes, which amount to greater than 10K gene sequences in the 60K or so rice genome. Still, scientists may wish to study the behavior of the whole gene family even if its individual family members cannot be uniquely identified. A new algorithm has been developed which allow highly similar genes to be grouped into families to select oligos for microarrays. PICKY 2.0, is now available for all major computing platforms and is distributed from our website at no charge to academic users.