Design Array - Frequently Asked Questions:
DR Noguera et al. (2014) "Mathematical tools to optimize the design of oligonucleotide probes and primers." Applied Microbiology and Biotechnology, doi:10.1007/s00253-014-6165-x.
Design Array chooses the optimal set of group-specific probes for identifying sequences using a DNA microarray. Probes are selected to optimize sensitivity and specificity for each target group.
The web tool provides a list of microarray probes that can be synthesized by many manufacturers onto a custom DNA microarray. Note that the model was originally calibrated using NimbleGen arrays. Although predictions are likely similar for other microarray platforms, hybridization conditions should always be experimentally optimized.
The downloadable program offers control over additional parameters, which makes it more flexible. For example, it allows specification of a region within the sequence alignment to target in probe design. Also, the DECIPHER package for R can handle larger tasks because it has no limit on the size of the sequence set or the number of groups.
The results are usually emailed to the user within a few hours of submission unless there is an unusually heavy server load at the time. Please check your spam filter if you do not receive results within a day, otherwise contact us.
The Design Array web tool does not permit multiple submissions in order to better share the server’s resources between users. New jobs may be submitted after receving the email with results from the prior submission.