Get FISH Probes from OligoPaints

Ting Wu's lab have developed a powerful tool OligoMiner for FISH probe designing. If you want to find probes for FISH, you can simply using the software, or using the online application OligoMinerApp.

We recommend to use OligoMinerApp, which is simple and customizable. However, if your Internet is awful and you disconnect with the server, you can use the probes database provided by Ting Wu's lab.

You will find database files listing the genomic locations of Oligopaints probes in the C. elegans (ce6 and ce11), Drosophila melanogaster (dm3 and dm6), Arabidopsis (tair10), Mouse (mm9 and mm10), Zebrafish (danRer10) and Human (hg19, hg38, and hg38U) genomes. What you need to do is download the database, then select probes in your gene's region manually. Each line in the database contains the probe's sequence, location in the chromosome. Spend time you will get them.

Here we wrote a simple script to skip the boring process.

Download the get_probes_from_OligoPaints zip file here, then unzip it. This is a simple script to help you get probes from oligopaints.

Example: I want to find probes for gene A, which is located in chromosome 1 from 1 to 114514.

1. Run the executable file, then drag the hg19_chr1b.bed file to the terminal, or input the database path.
2. Input gene's region. 
3. Probes will be saved as a csv file and a fasta file. In SnapGene, if you got the sequence of the gene, you can use "Primes -> import primers form a list " to import the fasta file as primer. Then you can see the probes are showed as primers and attached to the target sites.