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CHOPCHOP
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.
PROGNOS / Predicted Report Of Genome-wide Nuclease Off-target Sites
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.
SAPTA / Scoring Algorithm for Predicting TALEN Activity
Allows researchers to design highly active TALEs and TALENs to a target DNA sequence. For any input gene of interest, SAPTA gives a ranked list of potential TALEN target sites, facilitating the selection of optimal TALEN pairs based on predicted activity. SAPTA-based TALEN designs increased the average intracellular TALEN monomer activity by >3-fold, and resulted in an average endogenous gene-modification frequency of 39% for TALENs containing the repeat variable di-residue NK that favors specificity rather than activity. It is expected that SAPTA will become a useful and flexible tool for designing highly active TALENs for genome-editing applications.
E-TALEN
Allows transcription activator-like effector nucleases (TALEN) design of various scale. E-TALEN is a web service comprising two applications: (i) one for the design of de novo TALENs and (ii) one to re-analyse and re-evaluate existing TALEN designs in their genomic context. The software several features such as sequence and annotation databases for various organisms, rules for design optimization towards genome engineering purposes and scoring schemes for specificity and efficiency assessment and a system-independent interface.
QueTAL / Que Transcription Activator-Like
Offers tailored tools for comparison of Transcripton Activation-Like (TAL) effector genes to infer functional and evolutionary relationships. This toolkit contains two packages, DisTAL for distance calculating with repeated bases and Functal used to calculate distance thanks to DNA binding specificities. QueTAL analysis can rapidly study any TAL effector genes of interest and compare them to other available TAL genes. It also can classify groups of TAL effectors with similar DNA-binding specificities (targeting the same EBEs) or highlighting cases of functional convergence on key susceptibility genes.
TALENdesigner / Transcription Activator-Like Effector Nuclease designer
A toolkit for genome editing. TALENdesigner is based on a unique modular DNA-binding domain of TALEs from plant-pathogenic bacterial genus Xanthomonas. It enables the extension of genetic manipulations to virtually any model organisms and cell line. TALEN includes ligation-independent cloning and solid-phase cloning such as Fast Ligationbased Automatable Solid-phase High-throughput platform for large scale assembly of TALENs and Iterative Capped Assembly, the latter allowing for a rapid automatized robotic assembly with a high-throughput capability.
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