In order to design probes and primers for your microarray projects, you need to process a massive number of sequences and avoid cross homologies, which takes a considerable amount of time without the help of a specialized piece of software that can do it in a few minutes.
Perform online BLAST searches and design multiple probes
Array Designer is an application that greatly simplifies the probe and primer creation process for SNP detection projects, while also allowing you to perform optimized BLAST searches on local databases or by connecting directly to the NCBI. These searches ensure the signal fidelity and allow you to automatically avoid cross homologies for increased probe design optimization.
In addition, the created primers are optimized for identical PCR reaction conditions, while the probes can be designed in greater numbers per sequence, in order to increase the detection accuracy. The maximum length of a probe can reach 99bp and you can also create primers that amplify SNP sites.
Retrieve sequences online and export the results as spreadsheets
In order to include more sequences into your projects, you can either load them from a local computer, or connect to an online database such as Entrez or dbSNP and retrieve them using assay IDs and accession numbers. Furthermore, the supported file formats include the GenBank and FASTA extensions, which can also contain multiple sequences in the same document.
After you are done performing the desired searches, you can save the results and export them to an external file for further analysis, such as Microsoft Excel or Lotus 123. The spreadsheet form allows you to easily order and sort the desired values, as well as use them in a separate database or other piece of specialized software.
Although Array Designer is a very complex application aimed at experienced scientists working on large-scale projects, it does come with a lengthy and in-detail manual that explains how to make full use of the utility. In addition, you are provided with a quick tour presentation and various tutorials you can consult when you run into difficulties.