OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach.

ABSTRACT: There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally specific to their respective targets to avoid any cross-hybridization and should not form stable secondary structures that may interfere with the labeled probes during hybridization. We have developed OligoArray 2.0, a program that designs specific oligonucleotides at the genomic scale. It uses a thermodynamic approach to predict secondary structures and to calculate the specificity of targets on chips for a unique probe in a mixture of labeled probes. Furthermore, OligoArray 2.0 can adjust the oligonucl

SUBMITTER: Rouillard JM 

PROVIDER: S-EPMC162330 | biostudies-literature | 2003 Jun

REPOSITORIES: biostudies-literature