Popular oligo design

The purpose of "popular oligo design" is to select popular oligos, i.e., oligos that appear in as many sequences as possible, from a unigene dataset. The process contains three steps as shown in the following. Explanations of the terms involved can be found in the "help" page. A toy version of input data can be found in the "download" page.

Because the popular oligo design is a computation-intensive process, and due to the limitation of computational resources, we recommend you download the program from "download" page and run it locally if your input size is bigger than 50 MB.

Note: ONLY plain text files are accepted; please DO NOT upload Microsoft Word, Rich Text Format, or PDF files etc.


Step 1: Input unigene sequences

Upload unigenes in FASTA format (smaller than 50 MB):

Step 2: Selection and filtration parameters

Min color of cores (> 3) (Smallest # of distinct unigenes where an oligo's core occurs)
Min GC content (%) Max GC content (%)
Min melting temperature (° C) Max melting temperature (° C)


Step 3: Non-target sequences (that oligos shall not hybridize)

Select an internal DNA database

Or, upload your own FASTA file (smaller than 20 MB):


Step 4: Receiving output:

Oligos will be sent via email. Please input your email address:

It'll take a bit time to upload the file, please wait for a window with text confirming your email address. Thank you!