Design FISH Probes - Frequently Asked Questions
ES Wright et al. (2014) "Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification." Applied and Environmental Microbiology, doi:10.1128/AEM.01685-14.
Design Probes chooses the most specific FISH probes for targeting identification of a group of RNA sequences in the presence of multiple non-target groups. The tool generates two outputs, the first listing all possible single probes and the second listing the top 100 dual probe pairs. Dual probes can often be used in combination to achieve higher specificity of the target group.
Yes, Design Probes will choose probes matching the specified constraints with the fewest permutations to achieve maximal coverage of the target group. Simply submit a set of sequences that all share the same target group identifier.
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 non-target groups.