Willsey Lab, Institute of Neurodegenerative Diseases, UCSF

Design Your Primers

To start:
Upload a list of regions that need primers (max 5000; see below for example input):

About This Tool

This site uses Primer3 to generate PCR primer candidates for all genomic regions specified in your input file. For each input region, Primer3 is run twice with different criteria to increase the number of viable primers found. Each run yields a maximum of 20 primers. To ensure primer specificity, this tool tests primer candidates using a version of Jim Kent's in silico PCR. In addition, when making primers for hg19, genomic positions containing common SNPs (minor allele frequency > 5%) are excluded from primer sequences in order to reduce the chance of PCR failures.

Input File

To start, you must upload a tab-delimited text file. (To convert an Excel file, export it as "tab-delimited text.") The file should have columns for the chromosome (e.g., "chr7" or "7") and the start position (base coordinates) of all target regions. Including a stop position column guarantees that the entire region from start position to stop postion will be included in the primer product, up to a product size of 10,000bp. Since the minimum product size is 200 bases, the use of a stop position column is not always necessary. Any extra columns included in the input file will be ignored and re-printed in output. Using a header line will make the output more readable, but it's not required. (The use of multiple header lines is not allowed.)

Here's what an input file might look like:

StudyID		Chromosome	Position
101		chr3		54,881,527
102		chr9		24,000,020
103		chrX		5,043,122

In this example, the user should specify column 2 as the chromosome column and column 3 as the start column.
The optional stop column has been omitted, and the experiment-specific ID column is not relevant to this tool.

Output Files

The BestPrimers output file contains detailed information on the two best primer pairs found for each input region as determined by Primer3. Primers failing the isPCR test will not be included in this file, with one exception: Primers for sex chromosomes are allowed to match exactly one region on the opposite sex chromosome, and are marked in the XY_Oppo_Match field. (This field is irrelevant for genomes without sex chromosomes.) Both primers in the BestPrimers file will come from Run 1 of Primer3 unless that run yields fewer than two primer pairs, in which case primers will be taken from Run 2. For some reference genomes, particularly ones that are highly repetitive or not well characterized, it's possible that most primers will fail in-silico PCR. In that case, you may need to use the AllPrimers output file.

The AllPrimers file lists all primers returned by Runs 1 and 2 of Primer3 for all input regions, including primers that fail the isPCR test. Primers in this file are ordered by Primer ID, which follows the format chr_startPos_stopPos_RunNum_PrimerNum. The run number corresponds to Run 1 or Run 2 of Primer3, and Primer Number is a number from 1 to 20 assigned by Primer3. (Since Primer3 returns up to 20 primers per run per target region, these numbers are used to uniquely identify each pair of primers.)

The FailedRegions file lists all of the input regions for which no primers were printed in the BestPrimers file. Either Primer3 failed to find any primers, or all of Primer3's primers failed the isPCR test.

The Regions50 and Regions1000 files contain, for your convenience, the fasta sequences used by this tool for the 50- and 1000-base neighborhoods around the input file's target regions. See below for more information about the reference builds used by this tool.

Available genome builds

Primer3 Settings

This program runs Primer3 version 2.3.7 twice with different settings. Primer3 has hundreds of optional settings; any settings not listed in this tool's Run 1 and Run 2 settings files retain their default values. For details, see the Primer3 manual. If you would like, you can also upload your own Primer3 settings files, in which case you should keep these points in mind:

Data Security

The best practice is to assume that any files you upload to this site could be read by anyone. Therefore, do not include any type of sensitive or private information in your input file. If your input file has a lot of extraneous columns unrelated to primer design, it may be best to extract just the relevant columns before uploading.

Credits

This website was created by Jeff Mandell. The back-end script that does the work of designing primers using Primer3 and gfPcr was designed and implemented by Jeff Mandell, with advice from Michael Walker and Stephan Sanders.

Copyright Notice

Copyright (c) 2017, Regents of the University of California
All rights reserved.

Regents of the University of California are the proprietor of the copyrights of and to the Primer Designer website ("Content"). Redistribution and use of the Content with or without modification are permitted provided that redistributions of Content must retain the above copyright notice, list of conditions and the following disclaimer.

  1. Use of the Content for the sale of any product or service or for the purpose of profit-making is strictly prohibited.
  2. Any request to furnish all or any portion of the Content for the sale of any product or service or for the purpose of profit-making, shall be in writing to Director, Office of Innovation, Technology & Alliances, the University of California, San Francisco.
  3. The content uses third party resources listed below in i, ii, and iii ("Third Party Resources"). Certain licenses attach to Third Party Resources and by using Content you agree to abide by those licenses.
    1. Primer3, version 2.3.7 (license)
    2. gfServer/gfPcr (license)
    3. Reference genomes (license)

THIS CONTENT IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS", AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.