Picky: oligo microarray design for large genomes

Abstract

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.

A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum

“…Several oligomer design programs were tested (2, 4, 14, 15, 20, 28, 30-32, 40, 41, 43), and six programs (CommOligo [14], ROSO [28], YODA [20], ArrayOligoSelector [2], OligoWiz 2.0 [41], and PICKY [4]) were selected based on the higher numbers of criteria (e.g., the level of sequence identity, the number of contiguous matches, T m , and the level of free binding energy) employed by these programs than by the other programs to select each probe, the extent of available details for individual algorithms, and the ease of use per our assessment.…”

Knockdown of Lmo7 inhibits chick myogenesis

“…Second, siRNA evaluation was performed using NEXT-RNAI software [11], and siRNAs with best efficiency score were chosen for next step. Third, 19 selected siRNAs were examined by Picky and BLAST-NCBI Sequence Analysis Tool [2,14] to discover any potential off-target. The genome and cDNA sequences used during screening were obtained from Ensembl release 78.…”

Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data

“…As possible, to distinguish among the common targets, the NSF45K array and other publicly available rice arrays contain other oligos that probe unique regions of alternative splice forms. The NSF45K array was designed with the oligo identification tool PICKY 2.0 to distinguish 1,583 alternatively spliced transcripts through a combination of 3,430 shared and unique oligonucleotides [5,14]. By utilizing a combination of NSF45K array probe sets, we were able to explore the existence of alternative transcripts on a large scale and examine or deduce their expression patterns.…”

“…We used the oligonucleotide identification tool, PICKY 2.0, to design the 50-to 70-mer oligos that comprise the NSF45K array [5]. Because species with large genomes tend to contain large numbers of homologous genes, it is not possible to design long oligos capable of differentiating among all genes in these species [5,35]. The improved PICKY 2.0 includes a new feature that groups highly similar genes and designs oligos for the groups, including sets of alternatively spliced isoforms.…”

“…The improved PICKY 2.0 includes a new feature that groups highly similar genes and designs oligos for the groups, including sets of alternatively spliced isoforms. Using PICKY 2.0, we applied an oligonucleotide design stringency for all genes requiring less than 17 nucleotides exact match to any nontarget and a 10°C minimum separation of melting temperature between the highest affinity nontarget and the target (http://www.complex.iastate.edu/download/Picky/ Picky2_oligos/RiceOligos.html) [5]. These criteria led to the design of 43,311 oligonucleotide probes that target 45,116 gene models out of a total of 61,420 target transcript sequences in the TIGR/RGAP V3 rice gene set release.…”