Array Designer can automate the design of primers and probes for tiling arrays. With Array Designer, you can design tiling arrays to spot every base of a long genomic sequence while avoiding repetitive regions.
Array Designer helps you spot each and every base of the target DNA sequence using the 'Overlapping Amplicon' option. As the name suggests, this option outputs primers that produce overlapping amplicons so that no base pair is left undetected. The other option available for primer design is the 'Distinct Amplicon' option. The amplicons generated could be as close as one base pair apart, depending on the sensitivity you choose.
Array Designer can design both overlapping and non-overlapping primers to generate either distinct or overlapping amplicons for whole genome amplification depending on the desired sensitivity.
Array designer designs tiling arrays avoiding primer design in repetitive regions. These regions are masked using the "Repeat Masker". All the three output options (X, N and lower case) are recognized by Array Designer.
Array Designer designs evenly tiled probes across the genome which facilitate genome wide analysis of many important biological functions including sites of chromatin modification and sites of DNA methylation.
Genome-wide tiling arrays can overcome many of the limitations of the previous approaches by comprehensively probing transcription in all regions of the genome. Whole genome high density tiling arrays provide a universal platform for genomic analysis through whole genome amplification. Tiling microarrays through whole genome amplification allow you to explore other genome-wide structure/function relationships, including global studies of transcription factor binding sites, sites of chromatin modification, sites of DNA methylation and even chromosomal origins of replication.
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.