CRISPR Primer Designer

Clustered regularly interspaced short palindromic repeats – CRISPR associated system enables biologists to edit genome precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers and genome architecture.

CRISPR Primer Designer was developed for researchers to design primers for CRISPR applications. This program has a user-friendly interface, and can analyze the BLAST results by using multiple parameters and score for each candidate spacers, generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for CRISPR-Cas system based chromosome imaging system.

CRISPR Primer Designer Program Outline

Program Download

Release Beta Version: 1.1.2

NOTICE: When using Oryza sativa(rice) genomic data for BLAST on NCBI website, you can search [Oryza sativa (taxid:4530)]. If you are using the default Database: RefSeq Genomic, add NOT "scaffold" in the Entrez Query textbox, and then start BLAST. If you are using Database: Genome(IRGSP-1.0), add AND "IRGSP" in the Entrez Query textbox to use the new NCBI database(03-2016), or add AND "complete" in the Entrez Query textbox to use the old NCBI database(08-2012), and then start BLAST. We suggest that you could use the new featured Local BLAST function embeded in the program for BLAST, it's more easy and convinent. Thank you for using our program.

Please cite us: CRISPR Primer Designer: Design primers for knockout & chromosome imaging CRISPR-Cas system. J Integrative Plant Biology, 2015, DOI: 10.1111/jipb.12295

Update: v1.1.2 Beta

  1. Feature added: Local BLAST, program can execute BLAST tasks using local databases in addition to NCBI website BLAST. Local BLAST database can be built by this program. To active local BLAST, just make sure the checkbox of Local BLAST is checked.
  2. Database added: Arabidopsis.
  3. Database added: Rice.
  4. Feature added: Check update, program can detect the latest version of CRISPR Primer Designer.
  5. Interface changes: changed some fonts and size of the window to fit small screens.
  6. Bug Repaired: Program will not be forced to exit when loaded uncompleted result files.

Release Version: 1.0.1

Program manual

Download manual PDF File v.1.0.1

Organism Specifications

CRISPR Primer Designer should support all organisms that Whole Genome BLAST can excuted in NCBI, local BLAST or other sites with downloadable result files. Some organisms may not have a completed gemome assembly, unplaced scaffolds may lead to overlapping of target site which causing the rejection of the Specers. If those unplaced scaffolds cause so many rejections, you can take a risk by using those parameters below to exclude those scaffolds.

Download Organism Parameters

Program Requirements

Operation system(s): Windows XP or Higher

Microsoft .NET Framework version: 3.5 or higher

Click Here to download Microsoft .NET Framework

NOTE: the newest Microsoft .NET Framework version 4.5.X can’t be installed on Windows XP.

Help for Microsoft .NET Framework Installation

If you have any sugguestions, Please send us an E-mail: yanmeng@sibs.ac.cn.