ProbeDealer

This page includes resources published in our paper titled “ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization”. Reference: Mengwei Hu*, Bing Yang*, Yubao Cheng, Jonathan S.D. Radda, Yanbo Chen, Miao Liu & Siyuan Wang,¬†Scientific Reports, Volume 10, Number 22031, (2020). *Co-first authors. (Link).

Right click each link and use “Save link as” to download the following files as needed:
ProbeDealer package 
Human database (NEW updated to Gencode v37)
Mouse database (NEW updated to Gencode vM26)
Drosophila melanogaster database (NEW)
Honey bee transcriptome database (NEW)
Example target files
ProbeDealer user manual (Please follow the user manual to install a compatible BLAST version.)
Instruction for ordering dye-labeled secondary probes and primers

Conventional single-molecule RNA FISH (smRNA FISH) design
Besides probe design for multiplexed FISH experiments, ProbeDealer can be used to design FISH probes targeting individual RNA species for conventional single-molecule RNA FISH (smRNA FISH). This functionality may offer a cheaper alternative to commercial options of custom-target smRNA FISH. An instruction for how to use ProbeDealer for conventional smRNA FISH probe design is included here:
Instruction for using ProbeDealer for conventional smRNA FISH

Frequently asked questions and answers
Q: The Windows standalone version does not work. How to resolve the issue?
A: The “standalone” version actually still requires BLAST and a MATLAB runtime to be installed separately. Please strictly follow the installation instructions in the ProbeDealer user manual.

Q: ProbeDealer does not generate outputs. How to resolve the issue?
A: Try removing spaces in file paths or changing them into underlines. Try shortening the sequence header in your input target sequence fasta file, and removing spaces in the header.

Q: ProbeDealer shows a very long estimated design time for chromatin tracing probe design. How to resolve the issue?
A: We suggest the input sequence/coordinates for each chromatin tracing target segment (locus) not to exceed 100 kb. For example, one can input 40 segments of 100 kb each and efficiently design probes with ProbeDealer, but a single 4,000-kb segment as input will make the program run for a much longer time.