Principal Investigator: Gang Bao
Tools About tDnA Resources Software Tutorials FAQs

Scoring Algorithm for Predicting TALE(N) Activity

Compatible with Firefox, Chrome, and SafariNOT compatible with Internet Explorer

The Scoring Algorithm for Predicting TALEN Activity (SAPTA) allows researchers to design highly active TALEs and TALENs to a target DNA sequence.

If you have used SAPTA in the preparation of a paper, please cite it as described below:
Lin Y, Fine EJ, et al. SAPTA: a new design tool for improving TALE nuclease activity. Nucleic Acids Research,
doi:10.1093/nar/gkt1363 (2014).

To use this tool, simply enter the DNA sequence of the gene you are trying to target and press "Submit".
    Optionally, you may place brackets around the base you are trying to target: ACGT[T]GTA
        If brackets are used, numbers in the 'Starting Index' column will be positions relative to the specific nucleotide in brackets.
        For example, if you type in '..ACGT[T]GTA..', the start site '-3' means the target site starts 3 bases before (in the 5' direction of) the nucleotide in the brackets.
    To score multiple specified TALE binding sites, use the following FASTA-style input format (always beginning with the 5' base):
        >TALE 1
        >TALE 2
    To score multiple specified TALEN pairs, use the following FASTA-style input format:
        >TALEN pair 1
        >TALEN pair 2
    There is an initial limit of 1500 bp for the entry form and this amount will process fairly quickly on most computers. You may remove this limit if you choose.

The output consists of two components:
    A table showing the highest score for a TALEN pair beginning at each position in the DNA sequence. This can be copied into Excel to generate a graph.
    A table showing the highest scoring TALEs or TALENs in the DNA sequence. This can be copied into Excel to save your data.
        The 5' base is separated from the sequence targeted by the RVDs by a hyphen (Example: T-TACTGAAGTAACCT).
        In our hands, targeting a site with a composite score above 30 using NK to target G generally yields robust NHEJ rates above 20%.
        Sites with scores above 40 have been targeted successfully by us with endogenous NHEJ as high as 75%.
Additionally, for TALEN pairs, SAPTA will search to see if there is a unique restriction enzyme site in the spacer that can be used for RFLP analysis.

Search Type: TALEN Pair
Single TAL Effector
Score individual TAL binding site(s)
Score individual TALEN pair(s), optimal spacer length is assumed in score calculation

Require 5' T
Minimum Spacer Length
Maximum Spacer Length
Minimum TAL Repeat Array Length
Maximum TAL Repeat Array Length
Display up to Top TALEN sites

Display Advanced Settings

Enter a DNA sequence:

Mask redundant sites
Override the 1500 base pair limit?
Process the entirety of the sequence instead of just the top 50% of the TALENs?

The SAPTA TAL Targeter Tool was created by Corey Holman & Eli Fine
If you have comments, please email