TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction

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Date
2012
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Oxford University Press
Abstract
Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0; https://boglab.plp.iastate.edu/) that enables design of custom TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites, ranked by likelihood, in a genome, promoterome or other sequence of interest. Search parameters can be set by the user to work with any TAL effector or TAL effector nuclease architecture. Applications range from designing highly specific DNA targeting tools and identifying potential off-target sites to predicting effector targets important in plant disease.
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Keywords
bacterial protein, nuclease, nucleotide, transcription activator like effector, transcription factor, unclassified drug, binding site, computer interface, computer program, controlled study, DNA sequence, gene control, gene targeting, genetic engineering, genome editing, human, Internet, nonhuman, nucleotide binding site, nucleotide repeat, plant disease, prediction, priority journal, promoter region, promoterome, Algorithms, DNA, DNA-Binding Proteins, Protein Engineering, Repetitive Sequences, Amino Acid, Sequence Analysis, DNA, Trans-Activators, User-Computer Interface, nuclease, 9026-81-7, DNA, 9007-49-2
Citation
Doyle, E. L., Booher, N. J., Standage, D. S., Voytas, D. F., Brendel, V. P., Vandyk, J. K., & Bogdanove, A. J. (2012). TAL effector-nucleotide targeter (TALE-NT) 2.0: Tools for TAL effector design and target prediction. Nucleic Acids Research, 40(W1), W117-W122. http://dx.doi.org/10.1093/nar/gks608
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© The Author(s) 2012. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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