Engineered nucleases enable the targeted alteration of nearly any gene in a wide range of cell types and organisms. The newly-developed transcription activator-like effector nucleases (TALENs) comprise a nonspecific DNA-cleaving nuclease fused to a DNA-binding domain that can be easily engineered so that TALENs can target essentially any sequence. The capability to quickly and efficiently alter genes using TALENs promises to have profound impacts on biological research and to yield potential therapeutic strategies for genetic diseases.
Scans a DNA sequence for identifying potential zinc finger protein (ZFP) and zinc finger nuclease (ZFN) binding sites. ZiFiT is a web server that enables customizable searches for potential ZFP and ZFN-binding sites that can be targeted using either the modular assembly or OPEN engineering methods. The software also provides several tools to assist the evaluation of ZFP targets, such validated scoring schemes for ranking potential target sites, or a tool for querying NCBI BLAST servers for potential off-target sites.
Enables design of custom transcription activator-like (TAL) effector repeat arrays for desired targets as well as prediction of TAL effector binding sites. TALE-NT offers a suite of fours tools for TALEN and TAL effector design and target prediction that can be executed through a web application or locally downloaded. Moreover, the online interface provides users several “help pages” and tutorials, with guides for the interpretation of results.
A web tool for CRISPR- and TALEN-based genome editing. The overarching principle of CHOPCHOP is to provide an intuitive and powerful tool that can serve first time as well as experienced users. The basic mode offers optimized defaults for the basic user, while more advanced users can select from a wide range of options curated from the literature by their relevance and utility. All options are presented in a tabulated and organized manner to help users quickly visualize and evaluate options when designing CRISPR experiments.
Provides a user-friendly, web-based tool for rapid identification of potential nuclease off-target cleavage sites that can be evaluated using standard molecular biology techniques. The bioinformatics-based ranking algorithms in PROGNOS identify most nuclease off-target cleavage sites found by existing experimental methods. PROGNOS has relatively low false positive ratios and comparable false negative rates to experiment-based predictions, making it a robust method that can be readily implemented by most laboratories. Screening potential target sites using PROGNOS can facilitate the selection of superior nuclease target sites that minimize the number of likely genomic off-target sites. PROGNOS allows nuclease off-target analysis to become a routine component of nuclease design and testing, facilitating the discovery of new off-target sites for ZFNs and TALENs, which expand the off-target database and may improve future versions of the PROGNOS algorithms.
Investigates a sequence of interest to detect transcription activator-like (TAL) effector target sites. TALgetter is a computational method, available as both a web application and a command-line software, leaning on a distinct representation of repeat-variable diresidues (RVDs) weights and of their binding specificity. This program is able to handle files up to 90 Mb and also can be used to evaluate new model parameters from custom training data.