Print Email Facebook Twitter Mathematical design of prokaryotic clone-based microarrays Title Mathematical design of prokaryotic clone-based microarrays Author Pieterse, B. Quirijns, E.J. Schuren, F.H.J. van der Werf, M.J. TNO Kwaliteit van Leven Publication year 2005 Abstract Background: Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a random process, it is beforehand uncertain which genes are represented. Nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the library, can be predicted by mathematical approaches. When applying the classical formulas that determine the probability that a certain sequence is represented in a DNA library at the nucleotide level, massive amounts of clones would be necessary to obtain a proper coverage of the genome. Results: This paper describes the development of two complementary equations for determining the genome coverage at the gene level. The first equation predicts the fraction of genes that is represented on the array in a detectable way and cover at least a set part (the minimal insert coverage) of the genomic fragment by which these enes are represented. The higher this minimal insert coverage, the larger the chance that changes in expression of a specific gene can be detected and attributed to that gene. The second equation predicts the fraction of genes that is represented in spots on the array that only represent genes from a single transcription unit, which information can be interpreted in a quantitative way. Conclusion: Validation of these equations shows that they form reliable tools supporting optimal design of prokaryotic clone-based microarrays. © 2005 Pieterse et al; licensee BioMed Central Ltd. Subject BiologyBiotechnologygenomic DNAActinobacteriaarticlebacterial genomebacterial strainDNA libraryDNA microarrayEnterobacteriaceaeFirmicutesFusobacteriagene expressiongene insertiongene sequencegenetic transcriptionmathematical computingmolecular cloningnonhumanprokaryoteProteobacteriaspecies differencestatistical analysisstatistical significanceVibrionalesActinobacteriaBacteria (microorganisms)EnterobacteriaceaeFirmicutesFusobacteriaProkaryotaProteobacteriaVibrionales To reference this document use: http://resolver.tudelft.nl/uuid:0dda42f4-4058-4c9b-b292-938a9da33eef DOI https://doi.org/10.1186/1471-2105-6-238 TNO identifier 238719 ISSN 1471-2105 Source BMC Bioinformatics, 6 Article number No.: 238 Document type article Files To receive the publication files, please send an e-mail request to TNO Library.