Array Designer can be used to interrogate a gene/an exon or any other stretch of DNA of your choice. Here are the options available for whole genome array design that Array Designer presents:
Probes by Positions: To detect regions of interest on the entire genome.
Whole genome array experiments use array-based hybridization to scan the entire genome of an organism. The technology helps investigate expression levels of all genes, transcripts or a large fraction of the genome simultaneously with high reproducibility and sensitivity. This is achieved by using a set of overlapping oligonucleotide probes covering the entire genome.
The development of whole genome array represents another advancement critical to the development of new microarraying applications. Whole genome arrays have been useful for studying the poorly understood aspects of trancriptomes and natural antisense transcripts as they can simultaneously monitor gene expression on both strands of the genome. They have been found extremely useful for discovering novel genes.
Array Designer designs thousands of primers and probes for oligo and cDNA microarrays in seconds. It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available.
Array Designer designs highly specific oligos by interpreting the results of a BLAST search performed against any genomic database available at NCBI or a local custom database. Any significant homologies identified are automatically avoided while designing oligos. Repeat regions are identified and automatically avoided.