CRISPR Genome Analysis Tool

Welcome to the Iowa State University Crop Bioengineering Consortium's CRISPR Genome Analysis Tool.

This tool works in two steps:

  1. Identify potential target sites for CRISPR gene editing in DNA sequences
  2. Optionally, use identified target sequences from step 1 to search a genome of interest for potential off-target matches

Click here for publication citation

Please enter or select an input sequence
21 23

Analyze     Clear Input

  receiving {! progressCounter !} of {! progressMax !} search results finished processing {! progressMax !} searches
  strand length sequence unique position max repeat GC Content 3' Identity
(20 closest matches)
Input a sequence to search in the textarea above
Nothing found for provided input sequence and parameters
{! 1 + $index !} {! match.strand !} {! match.match.length !} {! match.normalizedMatch !} {! match.isUnique ? 'yes' : 'no' !} {! match.positions[0] !} – {! match.positions[1] !} {! match.maxRepeats !} {! match.cgContent !} %

How This Tool Works:
  1. For each genome available to search above, the genome sequence has been parsed in advance for valid CRISPR target sequences. All found target sequences were exported to a SQL database along with some relevant metadata. Additionally, the transcript data for each gene has also been stored in the SQL DB for easy retrieval when a user opts to select the input sequence from a specific gene.
  2. In the tool interface, Javascript is used to parse both the input sequence and its complement for valid CRISPR targets based on the user-provided search parameters (i.e., Target Length, GC Content and Allowed Nucleotide Repeats). The results are rendered in the browser and, for each found target sequence, a request is sent to the webserver to search the specified genome database for potential off-target matches.
  3. For each request sent from the web browser to the webserver in the previous step, the server queries the database for the target genome with the user-provided search parameters.
  4. Search results are filtered and sorted primarily by an identity score between an input subsequence (bases 6-18 for 21 base sequences or bases 6-20 for 23 base sequences) and the corresponding subsequences stored in the database. Additional sorting is performed based on an identity score between the subsequence at bases 2-5 of the input sequence and the corresponding subsequences in the database.
  5. Finally, the webserver returns the search results to the browser which updates the existing table. Clicking any table row reveals more details about the result.
Additional design features under development but not currently available include:
  • Graphical and tabular genomic position information for target & off-targets
  • Restriction Enzyme cut sites within targets
  • Currently the tool searches exclusively for 'G' as the first base on the five prime end of targets, we may consider expanding that to other nucleotides
  • Additional indexed genomes

Please report any questions or concerns about this tool to the administrator/developer

This tool uses genomic data from The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Genome Portal

Vincent A Brazelton Jr, Scott Zarecor, David A Wright, Yuan Wang, Jie Liu, Keting Chen, Bing Yang & Carolyn J Lawrence-Dill (2015)
A quick guide to CRISPR sgRNA design tools, GM Crops & Food, 6:4, 266-276, DOI: 10.1080/21645698.2015.1137690