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E-TALEN: a web tool to design TALENs for genome engineering.

Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, Boutros M - Nucleic Acids Res. (2013)

Bottom Line: Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics.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.

View Article: PubMed Central - PubMed

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.

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.

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E-TALEN workflow. The E-TALEN workflow can be divided into three parts: the web service/interface, the implemented design algorithm and the output in various file formats and an html report. The web service can be sub-divided into the two different aims of de novo design of TALENs against a specific target and the re-evaluation of existing TALENs to find/re-check their target or genomic context. Depicted on the right are the pre-calculated databases that supply the design algorithm with genomic or sequence information, enabling fast and efficient information management during the design procedure. The main part of E-TALEN consists of design algorithms that find and validate putative TALEN targets, followed by providing comprehensive information on resulting TALENs and their target sites. These two parts of the workflow are hidden from the user. The last part of the E-TALEN workflow is the generation of an output that comprises various computer and human-readable file formats, which are known from high-throughput sequencing, and a visual report shown in the user’s browser.
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gkt789-F1: E-TALEN workflow. The E-TALEN workflow can be divided into three parts: the web service/interface, the implemented design algorithm and the output in various file formats and an html report. The web service can be sub-divided into the two different aims of de novo design of TALENs against a specific target and the re-evaluation of existing TALENs to find/re-check their target or genomic context. Depicted on the right are the pre-calculated databases that supply the design algorithm with genomic or sequence information, enabling fast and efficient information management during the design procedure. The main part of E-TALEN consists of design algorithms that find and validate putative TALEN targets, followed by providing comprehensive information on resulting TALENs and their target sites. These two parts of the workflow are hidden from the user. The last part of the E-TALEN workflow is the generation of an output that comprises various computer and human-readable file formats, which are known from high-throughput sequencing, and a visual report shown in the user’s browser.

Mentions: If the user enters a gene symbol or ID, the associated sequence is retrieved from a genomic sequence database. Otherwise, the input sequence is read directly from the text entry. The input sequence is directly analysed for CpG islands and scanned for putative TALEN binding sites. To ensure that this search for binding sites is as effective as possible, three techniques are applied (Figure 1):


E-TALEN: a web tool to design TALENs for genome engineering.

Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, Boutros M - Nucleic Acids Res. (2013)

E-TALEN workflow. The E-TALEN workflow can be divided into three parts: the web service/interface, the implemented design algorithm and the output in various file formats and an html report. The web service can be sub-divided into the two different aims of de novo design of TALENs against a specific target and the re-evaluation of existing TALENs to find/re-check their target or genomic context. Depicted on the right are the pre-calculated databases that supply the design algorithm with genomic or sequence information, enabling fast and efficient information management during the design procedure. The main part of E-TALEN consists of design algorithms that find and validate putative TALEN targets, followed by providing comprehensive information on resulting TALENs and their target sites. These two parts of the workflow are hidden from the user. The last part of the E-TALEN workflow is the generation of an output that comprises various computer and human-readable file formats, which are known from high-throughput sequencing, and a visual report shown in the user’s browser.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814377&req=5

gkt789-F1: E-TALEN workflow. The E-TALEN workflow can be divided into three parts: the web service/interface, the implemented design algorithm and the output in various file formats and an html report. The web service can be sub-divided into the two different aims of de novo design of TALENs against a specific target and the re-evaluation of existing TALENs to find/re-check their target or genomic context. Depicted on the right are the pre-calculated databases that supply the design algorithm with genomic or sequence information, enabling fast and efficient information management during the design procedure. The main part of E-TALEN consists of design algorithms that find and validate putative TALEN targets, followed by providing comprehensive information on resulting TALENs and their target sites. These two parts of the workflow are hidden from the user. The last part of the E-TALEN workflow is the generation of an output that comprises various computer and human-readable file formats, which are known from high-throughput sequencing, and a visual report shown in the user’s browser.
Mentions: If the user enters a gene symbol or ID, the associated sequence is retrieved from a genomic sequence database. Otherwise, the input sequence is read directly from the text entry. The input sequence is directly analysed for CpG islands and scanned for putative TALEN binding sites. To ensure that this search for binding sites is as effective as possible, three techniques are applied (Figure 1):

Bottom Line: Use of transcription activator-like effector nucleases (TALENs) is a promising new technique in the field of targeted genome engineering, editing and reverse genetics.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.

View Article: PubMed Central - PubMed

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.

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.

Show MeSH
Related in: MedlinePlus