Picky: Oligo Microarray Design for Large Genomes
Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, and Patrick S. Schnable. Picky: Oligo Microarray Design for Large Genomes. Bioinformatics, 20: 2893 - 2902, Nov 2004.
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 www.complexcomputation.org
Lucy2: an interactive DNA sequence quality trimming and vector removal tool
Song Li and Hui-Hsien Chou. Lucy2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics, 20: 2865-2866, Nov 2004.
Summary: LUCY2 is a raw DNA sequence trimming and visualization tool based on the popular command-line LUCY1. Users can change parameters, trim multiple sequences and visualize the results within an integrated, easy-to-use graphical user interface. LUCY2 is designed specifically for non-programmers to use, and is currently available on Windows, Linux and MacOS X. Source code is also available for porting to the other platforms.
Availability: LUCY2 is distributed under the GNU General Public License and can be downloaded from www.complexcomputation.org