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NEXT-RNAi specifications

Information


Unique identifier OMICS_27396
Name NEXT-RNAi
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some sequence files and feature files.
Input format FASTA+TSV
Output data Some design information, a report including a graphical display of designs in GBrowse.
Output format TSV+HTML+FASTA+GFF+AFF
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
bowtie, primer3, blat, blast, mdust, ViennaRNA
Maintained Yes

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Maintainers


  • person_outline Michael Boutros <>
  • person_outline Thomas Horn <>

Publication for NEXT-RNAi

NEXT-RNAi in publications

 (4)
PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] evaluate, or reannotate existing rnai constructs (). these include up-torr for evaluation and visualization of existing rnai constructs (), rsvp for browsing and evaluating rnai stock phenotypes (), next-rnai for library design and evaluation (), and e-rnai, a web service for rnai construct design and evaluation (). these tools also implement algorithms that assess target specificity […]

PMCID: 5791663
PMID: 29199019
DOI: 10.1016/j.cels.2017.10.015

[…] uas-gal4 system (). rnai fly lines were crossed to hh-gal4 driver lines and kept at 25°c., for each gene, two ∼200 bp long sequence-independent double-stranded (ds) rna reagents were designed using next-rnai software (). the reagents were designed to avoid mismatches of 19 nt or more, more than 6 tandem tri-nucleotides of the can type, low complexity region or utrs. in a two-step approach (), […]

PMCID: 4831891
PMID: 26912791
DOI: 10.1091/mbc.E15-07-0467

[…] targeting ∼98% of all coding genes in the drosophila genome designed against flybase annotations for the drosophila melanogaster berkeley drosophila genome project genome, releases 4 and 5, using next-rnai software (). in addition, the library covered 1254 strongly expressed regions from the heidelberg predictions (heidelberg collection) of drosophila genes not covered by flybase (). primer […]

PMCID: 4384530
PMID: 25748138
DOI: 10.7554/eLife.05464.027

[…] (thermofisher) and 1% penicillin-streptomycin (thermofisher) as described previously (). two dsrnas of length 200–225 nt and non-overlapping in sequence were designed for each target gene using next-rnai software () and annotation from flybase release r5.24 (). the algorithm was designed to avoid perfect matches of length ≥19 nt or overall sequence similarity (blast e-value >10−10) […]


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NEXT-RNAi institution(s)
German Cancer Research Center (DKFZ), Div. of Signaling and Functional Genomics and University of Heidelberg, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany; University of Heidelberg, Hartmut Hoffman-Berling International Graduate School for Molecular and Cellular Biology, Heidelberg, Germany; University of Heidelberg, CellNetworks Cluster of Excellence, Heidelberg, Germany
NEXT-RNAi funding source(s)
Supported by a PhD fellowship by the Studienstiftung, in part by funding from the Deutsche Forschungsgemeinschaft, the Human Frontiers Sciences Program, the Helmholtz Association and the European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement n° 201666.

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