In addition to SNP detection and gene expression probes, Array Designer also designs probes for resequencing arrays. With custom resequencing arrays, you can detect SNP and other sequence variations in a large number of samples for applications such as biowarfare pathogen studies, predisposition and resistance to disease or discovering the genetic basis of phenotypic traits.
The challenge in designing chips for resequencing by hybridization is to achieve the lowest possible false positive rate. Array Designer offers an innovative and unique project BLAST capability to identify these regions and recommends a multi-chip solution.
You can simply connect to the popular Repeat Masker using the handy link and Array Designer will avoid creating spots that may generate false positives.
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.