title: E-TALEN: a web tool to design TALENs for genome engineering.
abstract: Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics. Its applications span from introducing knockout mutations to endogenous tagging of proteins and targeted excision repair. Owing to this wide range of possible applications, there is a need for fast and user-friendly TALEN design tools. We developed E-TALEN (http://www.e-talen.org), a web-based tool to design TALENs for experiments of varying scale. E-TALEN enables the design of TALENs against a single target or a large number of target genes. We significantly extended previously published design concepts to consider genomic context and different applications. E-TALEN guides the user through an end-to-end design process of de novo TALEN pairs, which are specific to a certain sequence or genomic locus. Furthermore, E-TALEN offers a functionality to predict targeting and specificity for existing TALENs. Owing to the computational complexity of many of the steps in the design of TALENs, particular emphasis has been put on the implementation of fast yet accurate algorithms. We implemented a user-friendly interface, from the input parameters to the presentation of results. An additional feature of E-TALEN is the in-built sequence and annotation database available for many organisms, including human, mouse, zebrafish, Drosophila and Arabidopsis, which can be extended in the future.
authors.affiliation: German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Heigwer
authors.forename: Grainne
authors.initials: G
authors.lastname: Kerr
authors.forename: Nike
authors.initials: N
authors.lastname: Walther
authors.forename: Kathrin
authors.initials: K
authors.lastname: Glaeser
authors.forename: Oliver
authors.initials: O
authors.lastname: Pelz
authors.forename: Marco
authors.initials: M
authors.lastname: Breinig
authors.forename: Michael
authors.initials: M
authors.lastname: Boutros
mesh_terms: D000818:Animals; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry*; D018390:Gene Targeting; D005818:Genetic Engineering; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; C035042:endodeoxyribonuclease FokI; D015252:Deoxyribonucleases, Type II Site-Specific