"With Array Designer, I was amazed at how easy it was to design primers for sequences from a cDNA library. I cloned the gene in a week. The homology avoidance algorithm works incredibly well, it made the probes so specific and my experiment a big success!" - Dr. Greg Khitrov, Gene Array Resource Center, The Rockefeller University, New York
"The primer selection process can be reduced from weeks to days" - HMS Beagle- Full review "...very useful tool for custom designing both cDNA and oligo arrays"- The Scientist- Full Review
Using Array Designer, you can design SNP probes for both hybridization and primer extension assays. Array Designer designs both wild and mutant probes. You can also design PCR primers for amplifying the SNP sites.
Load SNP: You can load thousands of SNPs for designing probes for SNP detection and genotyping. The SNPs can be defined as a variation feature in the GenBank file format. To load unpublished SNP information, you can reformat your sequence data to a GenBank like format with the help of the template provided, or you can add SNP information to sequences already loaded in a project with the Add SNP option.
Design SNP Hybridization Probes: For SNP detection assays, use the 'SNP at the center of probe' option to design wild and mutant probes. For primer extension assays, choose the '3' end one base upstream of SNP location' option. This functionality is useful for SNP genotyping.
Define Probe Output: You can design single or multiple probes, as required. For multiple probes, you can specify the sense (sense or anti-sense) and the minimum distance between the probes.
A Single Nucleotide Polymorphism (SNP) is the variation of a single base pair in the DNA sequence between either the members of a species or between the paired chromosomes of an individual. These polymorphisms may affect how organisms develop diseases and respond to chemicals and drugs. SNPs are, therefore, of great value in biomedical research and drug development. SNP detection and genotyping can be used to explain and diagnose many diseases, to study the variation in drug responses, to establish the origin of biological material and to study the relatedness between individuals.
Sequencing is a popular method for SNP genotyping but this method is more expensive and time consuming as compared to the microarray based methods. DNA microarrays represent a technological platform that enables SNP genotyping. Microarrays allow simultaneous testing of up to hundreds of SNPs.
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.