Local Tools

  • The EMBOSS programs: sirna - Finds siRNA duplexes in mRNA
    Available on sura (command line) or on the open in new windowourweb

siRNA Links And References

Web servers:

Chart:
Server Reference Rules Comments
Ambion 5 Tuschl No rank/score; link to NCBI Blast
Dharmacon 9, 13 Reynolds Score/Rank; Automatically runs blast
Can't see results or conditions of Blast
Clontech 5 Tuschl No score/rank; link to NCBI Blast
dsCheck 24 Checks for off target hits, new algorithm; currently for drosophila, c. elegans, arabidopsis, rice
OptiRNAi 2 Tuschl Score/Rank; Link to Genome Blast
Promega   Combination of Rules Link to NCBI Blast, no control over parameters
Qiagen   Tuschl Rules + extra parameters Score/Rank; Link to NCBI Blast, no control of parameters
siDirect 11, 17 Ui-Tei, option for custom rules No Score/Rank; Automatic Blast, private database,
no control over parameters, but can see results
open in new windowTROD 4   T7 specific; Link to NCBI Blast;
No score; highlighted rows preferable
MIT 22 Combined Tuschl and Reynolds, adjusted as necessary Requires pre-registration; configurable Blast of canditates;
Results sorted by thermodynamics

Resources (information):

Databases:

Selected References:

  1. Chalk AM, Wahlestedt C, Sonnhammer ELL. (2004) Improved and automated prediction of effective siRNA. BBRC 319:264-274
  2. Cui W, Ning J, Naik UP, Duncan MK. (2004) OptiRNAi, an RNAi design tool. Computer Methods and Programs in Biomedicine 75:67-73
  3. Ding Y, Chan CY, Lawrence CE. (2004) Sfold web server for statistical folding and rational design of nucleic acids. NAR 32:W135-W141
  4. Dudek P, Picard D. (2004) TROD: T7 RNAi Oligo Designer. NAR 32:W121-W123
  5. Elbashir SM, Harborth J, Weber K, Tuschl T. (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26:199-213
  6. Henschel A, Buchholz F, Habermann B. (2004) DEQOR: a web-based tool for the design and quality control of siRNAs. NAR 32:W113-W120.
  7. Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D, Labow M, Reinhardt M, Natt F, Hall J. (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol. 23:995-1001
  8. Huppi K, Martin SE, Caplen NJ. (2005) Defining and assaying RNAi in mammalian cells. Mol Cell. 17(1):1-10.
  9. Khvorova A, Reynolds A, Jayasena SD. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216
  10. Levenkova N, Gu Q, and Rux JJ. (2004) Gene specific siRNA selector. Bioinformatics 20(3):430-432.
  11. Naito Y, Yamada T, Ui-Tei K, Morishita S, Saigo K. (2004) siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. NAR 32:W124-W129
  12. Pancoska P, Moravek Z, Moll UM. (2004) Efficient RNA interference depends o global context of the target seqeunce: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA. NAR 32(4): 1469-1479
  13. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. (2004) Rational siRNA design for RNA interference. Nature Biotechnology 22(3):326-330
  14. Saetrom P, Snove O. (2004) A comparison of siRNA efficacy predictors. BBRC 321:247-253
  15. Saetrom P. (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20(17):3055-3063
  16. Takasaki S, Kotani S, Konagaya A. (2004) An Effective Method for Selecting siRNA Target Seqeunces in Mammalian Cells. Cell Cycle 3(6):790-795
  17. Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. NAR 32(3):936-948
  18. Vaucheret H. (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes and Development 20:759-771
  19. Wang L, Mu FY. (2004) A Web-based design center for vector-based siRNA and siRNA cassette. Bioinformatics 20(11):1818-20.
  20. Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH. (1998) Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs. Biochemistry 37:14719-14735
  21. Yiu SM, Wong PW, Lam TW, Mui YC, Kung HF, Lin M, Cheung YT. (2005) Filtering of Ineffective siRNAs and Improved siRNA Design Tool. Bioinformatics 21(2):144-151
  22. Yuan B, Latek R, Hossbach M, Tuschl T, Lewitter F. (2004) siRNA selection Server: an automated siRNA oligonucleotide prediction server. NAR 32:W130-W134
  23. Santoyo J, Vaquerizas JM, Dopazo J. (2005) Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics. 21(8):1376-82
  24. Yamada T, Morishita S. (2005) Accelerated off-target search algorithm for siRNA. Bioinformatics. 21(8):1316-24