Bioinformatic Tools

We develop database and computational tools for the design and analysis of high-throughput screening experiments.
Some of the tools are available as a web-based service for free.

The following tools have been developed within the lab:

 

E-CRISP - Design CRISPR reagents

E-CRISP

We developed E-CRISP to design CRISPR constructs and provide the possibility to alter various design parameters systematically. Currently E-CRISP is available for several different organisms, including mouse, rat, fish, fly, worm, Arabidopsis, yeast, human, frog, rice, medaka and more, providing the possibility to use it for different model organisms. E-CRISP identifies and evaluates potential CRISPR targets by a combination of options including specificity (should target one locus only), nucleotide composition, experimental purpose and genomic context (targeting a gene, specifying an exon, location in CpG island) among others.

Publication

Heigwer, F., Kerr, G., Boutros, M.
E-CRISP: fast CRISPR target site identification.
Nature Methods 11, 122-123 (2014). doi:10.1038/nmeth.2812

 

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E-CRISP

We developed E-CRISP to design CRISPR constructs and provide the possibility to alter various design parameters systematically. Currently E-CRISP is available for several different organisms, including mouse, rat, fish, fly, worm, Arabidopsis, yeast, human, frog, rice, medaka and more, providing the possibility to use it for different model organisms. E-CRISP identifies and evaluates potential CRISPR targets by a combination of options including specificity (should target one locus only), nucleotide composition, experimental purpose and genomic context (targeting a gene, specifying an exon, location in CpG island) among others.

 

Heigwer, F., Kerr, G., Boutros, M.
E-CRISP: fast CRISPR target site identification.
Nature Methods 11, 122-123 (2014). doi:10.1038/nmeth.2812

Fulltext

GenomeRNAi Database

GenomeRNAi is a database with phenotype information from high-throughput RNAi experiments in human (cell-based) and Drosophila (cell-based or in vivo). The GenomeRNAi website features search and browse functionalities, a “frequent hitter” page, download options, and a dynamic genome browser based on a DAS server. It is well integrated with external resources. The website also provides details on RNAi reagents and associated mapping information, as well as assessments with regard to their specificity and efficiency.

Direct submissions by data producers are welcome!

Schmidt, EE., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., Boutros, M. (2013).
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update.
Nucleic Acids Research 2013 Jan 1;41(D1):D1021-6. doi: 10.1093/nar/gks1170.

 Fulltext

genome-RNAi

E-TALEN

E-TALEN is a new web service to design TALENs for introducing knock-out mutations, endogenous tagging or targeted excision repair. The tool can be used to design TALENs against a single target or up to 50 target genes in parallel. E-TALEN guides the user through an end-to-end de-novo design process for specific sequences or genomic loci. It can also be used to evaluate existing TALEN designs.

Heigwer, F., Kerr, G., Walther, N., Glaeser, K., Pelz, O., Breinig, M., Boutros, M. (2013).
E-TALEN: a web tool to design TALENs for genome engineering.
Nucleic Acids Research 1-7 (2013). doi:10.1093/nar/gkt789

Fulltext

e-talen

E-RNAi

E-RNAi is a web application to design optimized RNAi reagents. It integrates genomic context information with predicted specificity and efficiency parameters.
E-RNAi can be accessed at e-rnai.org
Please cite when using E-RNAi: Horn, T., Boutros, M. (2010). E-RNAi: a web application for the multi-species design of RNAi reagents – 2010 update. Nucleic Acids Research 38:W332-339. Fulltext

NEXT-RNAi

NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries. It performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context.
NEXT-RNAi can be accessed at www.nextrnai.org and is available for download at GitHub.
Please cite when using NEXT-RNAi: Horn, T., Sandmann, T., Boutros., M. (2010). Design and evaluation of genome-wide libraries for RNAi screens. Genome Biology 11:R61. Fulltext

cellHTS

cellHTS is a software package implemented in Bioconductor/R to analyze cell-based high-throughput RNAi screens. The cellHTS2 package is the new version of the cellHTS package, offering improved functionality for the analysis and integration of multi-channel screens and multiple screens.
More information on cellHTS can be found at: www.dkfz.de/signaling/cellHTS
Please cite when using cellHTS: Boutros, M., Bras, L., Huber, W. (2006). Analysis of cell-based RNAi screens. Genome Biology, 7:R66. Fulltext

webcellHTS

A prototype of a web-application that provides a user-friendly interface to cellHTS and a step-by-step tutorial how to use cellHTS for the analysis of high-throughput screening experiments. web cellHTS is available as open source and can be downloaded for local installation.
web cellHTS is accessible at web-cellhts2.dkfz.de and available for download at GitHub.
Please cite when using web cellHTS: Pelz., O., Gilsdorf, M., Boutros, M. (2010). web cellHTS2: A web application for the analysis of high-throughput screening data. BMC Bioinformatics 11:185. Fulltext

Booking Calendar

A reservation management system for booking of lab equipment. Available for download at GitHub.

Please contact us with any suggestions or comments at b110-office (at) dkfz.de

 

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