WMD 3.2 – Web MicroRNA Designer

WMD 3.2

:: DESCRIPTION

WMD3 is a web app for the automated design of artificial microRNAs.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • Perl
  • gcc
  • MySQL
  • GenomeMapperBlast,
  • ViennaRNA

:: DOWNLOAD

 WMD

:: MORE INFORMATION

Citation

Plant Cell. 2006 May;18(5):1121-33. Epub 2006 Mar 10.
Highly specific gene silencing by artificial microRNAs in Arabidopsis.
Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D.

WU-CRISPR – WashU gRNA Designer for CRISPR/Cas9 Knockout

WU-CRISPR

:: DESCRIPTION

WU-CRISPR is the Washington University gRNA designer for CRISPR/Cas9 knockouts.

::DEVELOPER

Xiaowei Wang Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WU-CRISPR

:: MORE INFORMATION

Citation

WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system.
Wong N, Liu W, Wang X.
Genome Biol. 2015 Nov 2;16(1):218. doi: 10.1186/s13059-015-0784-0.

CSGM Designer – Cross Species Genic Marker Designer

CSGM Designer

:: DESCRIPTION

CSGM Designer has been developed with purposes of facilitating easy and systematic design of cross-species genic markers.

::DEVELOPER

CSGM Designer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.
Kim JH, Lee C, Hyung D, Jo YJ, Park JS, Cook DR, Choi HK.
Plant Methods. 2015 Apr 18;11:30. doi: 10.1186/s13007-015-0074-6.

DSIR – Designer of Small Interfering RNA

DSIR

:: DESCRIPTION

DSIR is a tool for siRNA (19 or 21 nt) and shRNA target design.

::DEVELOPER

DSIR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(10):e48057. doi: 10.1371/journal.pone.0048057.
DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes.
Filhol O, Ciais D, Lajaunie C, Charbonnier P, Foveau N, Vert JP, Vandenbrouck Y.

SGAtools 20131030 – Web-based Analysis System for Designer Genetic Screens

SGAtools 20131030

:: DESCRIPTION

SGAtools offers a single stop solution for analysing data from genetic screens. There are three steps to the analysis pipeline, each of which can also be run separately from the rest. First, images of plates with colonies are processed to give quantified colony sizes for the screen. Next, the colony sizes are normalised and filtered within plates, taking into account position effects and other confounding factors.

::DEVELOPER

Boone lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 SGAtools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul 1;41(Web Server issue):W591-6. doi: 10.1093/nar/gkt400. Epub 2013 May 15.
SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.
Wagih O, Usaj M, Baryshnikova A, Vandersluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L.