Abstract |
PICKY: Oligo Microarray Design for Large Genomes
Motivation: Many large genomes are getting sequenced nowadays. Biologists
are eager to start microarray analysis taking advantage of all known genes
of a species, but existing microarray design tools were very inefficient for
large genomes. Also, many existing tools operate in a batch mode that does
not assure best designs.
Results: PICKY is an efficient oligo microarray design tool for large
genomes. PICKY integrates novel computer science techniques and the best
known nearest-neighbor parameters to quickly identify sequence similarities
and estimate their hybridization properties. Oligos designed by PICKY are
computationally optimized to guarantee the best specificity, sensitivity and
uniformity under the given design constrains. PICKY can be used to design
arrays for whole genomes, or for only a subset of genes. The latter can
still be screened against a whole genome to attain the same quality as a
whole genome array, thereby permitting low budget, pathway-specific
experiments to be conducted with large genomes. PICKY is the fastest oligo
array design tool currently available to the public, requiring only a few
hours to process large gene sets from rice, maize or human.
Availability: PICKY is independent of any external software to execute,
is designed for non-programmers to easily operate through a graphical user
interface, and is made available for all major computing platforms (e.g.,
Mac, Windows and Linux) at http://www.complex.iastate.edu.
Reference:
Chou HH, Hsia AP, Mooney DL, Schnable PS. (2004). PICKY: oligo microarray
design for large genomes. Bioinformatics. EPub June 4, 2004.
The paper is available at http://bioinformatics.oupjournals.org/cgi/reprint/bth347v1
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