Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

Background: The design of long oligonucleotides for spotted DNA microarrays requires detailed attention to ensure their optimal performance in the hybridization process. The main challenge is to select an optimal oligonucleotide element that represents each genetic locus/gene in the genome and is unique, devoid of internal structures and repetitive sequences and its Tm is uniform with all other elements on the microarray. Currently, all of the publicly available programs for DNA long oligonucleotide microarray selection utilize various combinations of cutoffs in which each parameter (uniqueness, Tm, and secondary structure) is evaluated and filtered individually. The use of the cutoffs can, however, lead to information loss and to selection of suboptimal oligonucleotides, especially for genomes with extreme distribution of the GC content, a large proportion of repetitive sequences or the presence of large gene families with highly homologous members. Results: Here we present the progr...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser, Zbynek Bozdech
• Keywords: BMCBI 2007, Genome, Oligonucleotide, Repetitive Sequences