Tag: siRNA

siDirect 2.0 – Target Specific siRNA online Design Site

siDirect 2.0

:: DESCRIPTION

siDirect is a web server for providing efficient and target-specific siRNA design for mammalian RNAi. In this new version, the siRNA design algorithm has been extensively updated to eliminate off-target silencing effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability of the ‘seed’ duplex.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.
Naito Y, Yoshimura J, Morishita S, Ui-Tei K.
BMC Bioinformatics. 2009 Nov 30;10:392. doi: 10.1186/1471-2105-10-392.

DEsi – Design Engine of siRNA

DEsi

:: DESCRIPTION

DEsi is an siRNA design tool that quickly selects siRNAs with high RNAi activity against a desired mRNA.

::DEVELOPER

Natural Computing and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Po-Chang Chang, Wei-Jie Pan, Chi-Wei Chen,Yu-Ting Chen and Yen-Wei Chu(2012)
DEsi: an design engine of siRNA that integrates SVMs prediction and feature filters,
Biocatalysis and Agricultural Biotechnology, doi: 10.1016/j.bcab.2012.01.005

siPRED – Predicting siRNA Efficacy using Various Characteristic Methods

siPRED

:: DESCRIPTION

siPRED utilizes two layers of support vector regression (SVR) to predict the efficacy of an siRNA.

::DEVELOPER

Natural Computing and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

siPRED: predicting siRNA efficacy using various characteristic methods.
Pan WJ, Chen CW, Chu YW.
PLoS One. 2011;6(11):e27602. doi: 10.1371/journal.pone.0027602

TargetRank 1.0 – Rank Conserved and non-conserved microRNA Targets and siRNA off-targets

TargetRank 1.0

:: DESCRIPTION

 TargetRank is a webtool for ranking conserved and non-conserved microRNA targets and siRNA off-targets.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.G. (2007).
Determinants of targeting by endogeno us and exogenous microRNAs and siRNAs.
RNA 13, 1894-1910.

desiRm – Designing siRNA for Silencing a Gene

desiRm

:: DESCRIPTION

desiRm is a webserver for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.

::DEVELOPER

desiRm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(8):e23443. doi: 10.1371/journal.pone.0023443. Epub 2011 Aug 10.
Designing of highly effective complementary and mismatch siRNAs for silencing a gene.
Ahmed F1, Raghava GP.

RNAxs – Design Potent siRNAs

RNAxs

:: DESCRIPTION

RNAxs is a tool especially created to design potent siRNAs.

RNAxs Online Version

::DEVELOPER

Hakim Tafer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNAxs

:: MORE INFORMATION

Citation

Nat Biotechnol. 2008 May;26(5):578-83. Epub 2008 Apr 27.
The impact of target site accessibility on the design of effective siRNAs.
Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL.

OligoWalk 2 – Select Efficient siRNA using Hybridization Thermodynamics

OligoWalk 2

:: DESCRIPTION

OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence.

::DEVELOPER

Mathews group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OligoWalk

:: MORE INFORMATION

Citation:

Efficient siRNA selection using hybridization thermodynamics
Zhi John Lu and David H. Mathews
Nucl. Acids Res. (2008) 36 (2): 640-647