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

@article{citeulike:586192, 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 oligonucleotide length, according to user input, to fit a narrow Tm range compatible with hybridization requirements. Combined with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on cDNA or oligonucleotide libraries. OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93\% of these transcripts. 10.1093/nar/gkg426}, author = {Rouillard, Jean-Marie and Zuker, Michael and Gulari, Erdogan }, citeulike-article-id = {586192}, doi = {10.1093/nar/gkg426}, journal = {Nucl. Acids Res.}, keywords = {array, probe}, month = {June}, number = {12}, pages = {3057--3062}, posted-at = {2008-02-18 14:55:52}, priority = {5}, title = {OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach}, url = {http://dx.doi.org/10.1093/nar/gkg426}, volume = {31}, year = {2003} }

TY - JOUR ID - citeulike:586192 L3 - citeulike-article-id:586192 TI - OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach JF - Nucl. Acids Res. VL - 31 IS - 12 SP - 3057 EP - 3062 N2 - 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 oligonucleotide length, according to user input, to fit a narrow Tm range compatible with hybridization requirements. Combined with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on cDNA or oligonucleotide libraries. OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts. 10.1093/nar/gkg426 KW - array KW - probe AU - Rouillard, Jean-Marie AU - Zuker, Michael AU - Gulari, Erdogan PY - 2003/06/15/ UR - http://dx.doi.org/10.1093/nar/gkg426 ER -