Technique / Molecular Biology / RNAi siRNA gene silencing / siRNA design

Vector based siRNA design tool software
Tools include: *siRNA Target Finder: A software tool to identify unique candidate siRNA target sequence in your cDNA sequence. * siRNA Construct Builder: A software tool to build small hairpin insert from siRNA target for expression vector. * siRNA Sequ ...

siRNA design tool using SVM new software
A free online siRNA design tool using supporting vector machine algorithm (Chang bioscience). Features: 1.Rational siRNA design by rules and by SVM learning. 2.Designs oligos for a variety of tech platforms. 3.Eliminates unintended targets. 4.Avoids S ...

shRNA oligos design tool for shRNA based expression vector software
A free online siRNA design tool (Gene Link inc.). The guidline for using this tool is given in this link: siRNA Design Strategies: The strategy for siRNA design is based on our present understandi ...

The design and exogenous delivery of siRNA for post-transcriptional gene silencing software
siRNA target finder online tool (Ambion) This tool employs the early, basic siRNA design guidelines first described by Tuschl and colleagues. In general, Ambion scientists find that ~50% of ...

siRNA selector tool from wistar institute new software
Computing tool provided by Wistar Institute, University of Pennsylvania. A set of rules was used for evaluating siRNA functionality based on thermodynamics parameters (Khvorova A et al., 2003, Schwarz et al 2003) and sequence-related determinants developed ...

Sfold web tool: siRNA, antisense, trans-cleaving ribozymes design tool new software
Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. References: Ding, Y., Chan, C.Y., and Lawrence, C.E. (2004) Sfold web server for statistical foldi ...

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siRNA design methods and algorithms
(Curr Protoc Bioinformatics)
1: Curr Protoc Bioinformatics. 2004 Sep;Chapter 12:Unit 12.3.

RNAi: design and analysis.

Sachidanandam R.

Sachidanandam Lab, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York,
USA.

RNAi is a novel genetic tool that is poised to revolutionize the study of
genetics and gene networks. Use of this tool requires knowledge of the underlying
mechanisms and application of this knowledge to the construction of a
gene-silencing library. This unit discusses approaches to rational design of this
library and its use in experiments. It focuses on the design algorithms developed
so far and briefly discuss several issues that could lead to improvements in the
current design algorithms.

2: Curr Protoc Bioinformatics. 2006 Mar;Chapter 12:Unit 12.1.

An overview of RNA structure prediction and applications to RNA gene prediction
and RNAi design.

Stormo GD.

Washington University School of Medicine, St. Louis, Missouri, USA.

This unit briefly describes the two fundamentally different methods for
predicting RNA structures. The first is to find that structure with the minimum
free energy of folding, as predicted by various thermodynamic parameters related
to base-pair stacking, loop lengths, and other features. If one has only a single
sequence, this thermodynamic approach is the best available method. The second
fundamental approach to RNA structure prediction is to use multiple, homologous
sequences for which one can infer a common structure, and then try and predict a
structure common to all of the sequences. Such an approach is referred to as a
comparative method or phylogenetic method of RNA structure prediction.

(Selected siRNA design papers)
1: Gong W, Ren Y, Xu Q, Wang Y, Lin D, Zhou H, Li T.
Integrated siRNA design based on surveying of features associated with high RNAi effectiveness.
BMC Bioinformatics. 2006 Nov 27;7:516.

2: Naito Y, Ui-Tei K, Nishikawa T, Takebe Y, Saigo K.
siVirus: web-based antiviral siRNA design software for highly divergent viral
sequences.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W448-50.

3: Shabalina SA, Spiridonov AN, Ogurtsov AY.
Computational models with thermodynamic and composition features improve siRNA
design.
BMC Bioinformatics. 2006 Feb 12;7:65.

4: Scherer L, Rossi JJ.
Therapeutic applications of RNA interference: recent advances in siRNA design.
Adv Genet. 2004;52:1-21. Review. No abstract available.

5: Yiu SM, Wong PW, Lam TW, Mui YC, Kung HF, Lin M, Cheung YT.
Filtering of ineffective siRNAs and improved siRNA design tool.
Bioinformatics. 2005 Jan 15;21(2):144-51. Epub 2004 Aug 27.

6: Naito Y, Yamada T, Ui-Tei K, Morishita S, Saigo K.
siDirect: highly effective, target-specific siRNA design software for mammalian
RNA interference.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W124-9.

7: Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A.
Rational siRNA design for RNA interference.
Nat Biotechnol. 2004 Mar;22(3):326-30. Epub 2004 Feb 1.