Thermodynamically optimal whole-genome tiling microarray design and validation.
BACKGROUND
Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations.


RESULTS
Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome.


CONCLUSIONS
This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
Hyejin
H
Cho
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA. hhchou@iastate.edu.|Department of Computer Science, Iowa State University, Ames, IA, 50011, USA. hhchou@iastate.edu.
Hui-Hsien
http://orcid.org/0000-0002-2029-8743
HH
Chou
D016960:Agrobacterium tumefaciens / Q000235:genetics / Q000254:growth & development; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D016678:Genome / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods; D006863:Hydrogen-Ion Concentration; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012329:RNA, Bacterial / Q000235:genetics; D015203:Reproducibility of Results; D013045:Species Specificity; D013696:Temperature; D013816:Thermodynamics
D012329:RNA, Bacterial
Hybridization; Microarray validation; PICKY software; Prokaryote transcriptome; Thermodynamics; Tiling microarray design