Probe designer

This program takes an input sequence (such as an mRNA coding sequence) and will give as output a set of probes that are designed for optimal binding properties to this target RNA sequence (see notes at bottom). It will give a probe list as well as a graphical representation of where the different probes bind along the target sequence. You can then copy that page to a text file. Just be sure to change to a monospace font like Courier to preserve the spacing properties. Enjoy!.

Probe name:

Target sequence:
Enter sequence here

Number of probes:

Target GC%:

Oligonucleotide length:

Spacing length:

E-mail:

Some notes

• We typically input the ORF of the gene of interest and exclude the UTRs.
• Probes are designed to minimize deviations from the specified target GC percentage.
• The program will output the maximum number of probes possible up to the number specified.
• Sequence input is stripped of all non-sequence characters.
• We have had the most success with target GC contents of 45%.
• We have gotten good results using oligos of length 20 with a minimum 2 base spacing between oligos.