EENdb - EEN Engineering Resources
This page describes and links to the resources and web-tools of EEN engineering.
For description and comparison of the EEN construction strategies and methods, please see relevant pages of Utilities:
Quick links to frequently used web-sites
TALE-NT   ZiFiT   ZFNSiTer   TALengineering.org  



Candidate TALEN / TALE target site prediction
Tool & LinkTypeDescriptionReference
TALE-NT
(TAL Effector Nucleotide Targeter 2.0)
(Recommended)
TALEN/TALE TALE-NT is designed to search for TALEN targets in query sequences, with any repeat length and spacer length.
Multiple features are provided, such as finding restriction enzyme sites in TALEN spacer (for efficiency detection) and e-mail notification.
Requires a T (or sometimes C) at position 0 (i.e., immediately adjacent to the 5'-end of the half-site), and provide a choice to use 4 other suggested rules (these rules are not recommended by the authors of ZiFiT).
Downloadable software provided.
21493687
ZiFiT
(Zinc Finger Targeter 4.1)
(Recommended)
TALEN ZiFiT is originally designed to search for ZFN targets; now it also supports TALEN target site prediction.
The lengths of TALE repeat units and spacer are set for the application of certain TALEN construction methods, including REAL, REAL-Fast and FLASH.
ZiFiT only requires a T at position 0 (i.e., immediately adjacent to the 5'-end of the half-site) without other rules.
20435679
idTALE
(in silico designer TALEs)
TALEN/TALE idTALE can search TALEN sites in query sequences or genes by inputting IDs of certain species.
The lengths of TALE repeat units and specified by users, but the left and right half-site must have the same length.
22271303


Candidate ZFN / ZFP target site prediction
Tool & LinkTypeDescriptionReference
ZFNSiTer
(ZFN Integration Targeter)
(Recommended)
ZFN ZFNSiTer is based on and collaborated with EENdb. It integrated all public available (non-comericial) ZFN construction strategies, including MA, OPEN, CoDA, "PRS" and others as well as known ZFPs listed in EENdb, and also the combination of these strategies, for target site searching and prediction, with nearly no limitation of spacer length.
ZFNSiTer also provides a solution for the design of oligos or zinc-finger pool of these strategies.
(The work of EENdb)
ZiFiT ZFN/ZFP (Also described above)
ZiFiT supports CoDA and OPEN strategies.
The spacer length is restricted to 5-7 bp.
20435679
Wolfe's group (1F & 2F MA system) ZFN Predicting and scoring candidate ZFN target sites for the 2F-MA strategy using a module set generated by Wolfe's group.
22543349
(Lawson-Wolfe MA system) ZFN Predicting and scoring candidate ZFN target sites for the MA strategy using a module generated by Lawson's and Wolfe's groups.
21937602
ZFN Sequence Tag ZFN Directly searching candidate ZFN target sites of zebrafish genes in a pre-predicted database.
These candidate target sites can be constructed by MA strategy using a module set generated by Lawson's and Wolfe's groups.
21937602
("PRS") ZFN Searching for candidate ZFN target sites rich in purines (especially guanines), which might be screened and constructed by "PRS" strategy.
20843781
Zinc Finger Tools ZFP Not designed for ZFN target prediction.
Support searching for 6-24 bp (2-8 triplets) ZFP target sites by MA strategy.
16845061


EEN target (T) & off-target (OT) site finder
Tool & LinkTypeDescriptionReference
TALE-NT TALE - T/OT (Also described above)
Searching for single TALE target or candidate off-target sites of a series of known RVDs, in user provided sequence or some specific genomes/promoteromes.
Using a score cutoff to filter the candidate OTs.
21493687
idTALE TALEN - T (Also described above)
Searching for paired TALEN target site of a series of known RVDs in some specific genomes.
22271303
TagScan TALE/ZFP - T/OT Searching for targets and off-targets (maximum 2 mismatches) of a given single target sequence in certain genomes.
The input sequence can be TALE or ZFP target.
17593978
The ZFN-Site TALEN/ZFN - T/OT (Based on TagScan)
Searching for targets and off-targets (maximum 2 mismatches per half-site) of a pair of target sequences in certain genomes.
The input sequence can be a TALEN or a ZFN target.
21569489


Sources of protocols and materials
Site & LinkTypeDescription
TALengineering.org    TALEN/TALE The home site of FLASH, REAL and REAL-Fast platform.
TAL Effectors TALEN/TALE Protocols for "GG-PCR".
Addgene (TALEN) (REAL & REAL-Fast) TALEN/TALE Kits and plasmids for REAL and REAL-Fast; part of reagents and vectors for FLASH.
An NIH-sponsor project for targeting endogenous zebrafish genes by TALENs.
(GG) TALEN/TALE Kits and protocols for GG (V&B).
("GG-PCR") TALEN/TALE Kits and protocols for "GG-PCR".
Addgene (ZFC) ZFN/ZFP Plasmids for MA with module sets generated by Barbas, Sangamo and ToolGen; part of reagents and vectors for OPEN.
An NIH-sponsor project for targeting endogenous zebrafish genes by ZFNs. Now it has been replaced by TALENs.
Wolfe's group (1F & 2F MA system) ZFN/ZFP (Also described above)
Protocols and plasmids for 2F-MA strategy with the module set generated by Wolfe's groups.
(Lawson-Wolfe MA system) ZFN/ZFP (Also described above)
Protocols and plasmids for MA strategy with the module set generated by Lawson's and Wolfe's groups.
("PRS") ZFN/ZFP (Also described above)
Protocols for "PRS" strategy as well as a B1H selection system.


Other EEN related web-sites
Site & LinkDescription
Scoop.it! Information and news of TALE.
Google Groups Newsgroup of TALEN managed by Joung's group.
TAL Effectors TAL Effectors also provided news and interaction to users.
ZFC    Zinc Finger Consortium.
Mojo Hand (EENdb Updating...)





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