siRNA Links And References

Server Reference Rules Comments
Ambion 5 Tuschl No rank/score; link to NCBI Blast
Dharmacon 7, 11 Reynolds Score/Rank; Automatically runs blast
Can't see results or conditions of Blast
Clontech 5 Tuschl No score/rank; link to NCBI Blast
Deqor 6 Own set of Rules Built for siRNA and esiRNA; Score/Rank; Automatically runs Blast,
can control conditions, see results;
dsCheck 21 Checks for off target hits, new algorithm; currently for drosophila, c. elegans, arabidopsis, rice
EMBOSS 5 Tuschl Score/Rank; No Blast
Filter Ineffective siRNAs 18   Checks results of 11 other programs; checks secondary structure;
No Blast (unless part of another program)
GenScript 16 Combination of Tuschl, Reynolds, Ui-Tei Score/Rank; Blast/Smith Waterman vs.
proprietary database of EST + mRNA
Hannon Lab     No Score/Rank; No explanations of method
IDTDNA   Tuschl, Fire, Unified Rank, but no score; Can add/create pattern or rule; Link to NCBI Blast
Interagon 13 Allows use of 8 different algorithms Requires registration; Blast performed automatically
against Mouse Ensembl transcripts only;
Invitrogen   Tuschl or Proprietary Rank, no score; Automatically runs blast,
no option to control, but can see results
Jack Lin   Tuschl Link to NCBI Blast; output sorted by overhang and %GC
OptiRNAi 2 Tuschl Score/Rank; Link to Genome Blast
Promega   Combination of Rules Link to NCBI Blast, no control over parameters
Qiagen (Xeragon)   Tuschl Rules + extra parameters Score/Rank; Link to NCBI Blast, no control of parameters
SFold 3 Combination of folding, Reynolds, Tuschl Score, no rank; No Blast
SiDE 20 Combination of different rules Built for high throughput (No option to add seqeunce, just accession numbers); checks blast against Ensembl transcripts
siDirect 9, 15 Ui-Tei, option for custom rules No Score/Rank; Automatic Blast, private database,
no control over parameters, but can see results
siRNA wizard   Mixed Rules Gives top 10, with "recommended" in blue;
automatic blast against local mRNA datbase
siSearch 1 Stockholm Rules, also Ui-Tei, Amarzguioui and Prydz, Reynolds, allows custom rules various output formats; Blast with choices;
TROD 4   T7 specific; Link to NCBI Blast;
No score; highlighted rows preferable
Whitehead 19 Combined Tuschl and Reynolds, adjusted as necessary Requires pre-registration; configurable Blast of canditates;
Results sorted by thermodynamics
Wistar 8 Reynolds and thermodymanic considerations Score/Rank; Link to (unigene) Blast; results emailed

Web servers:

Resources (information):


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. Khvorova A, Reynolds A, Jayasena SD. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216
  8. Levenkova N, Gu Q, and Rux JJ. (2004) Gene specific siRNA selector. Bioinformatics 20(3):430-432.
  9. 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
  10. 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
  11. 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
  12. Saetrom P, Snove O. (2004) A comparison of siRNA efficacy predictors. BBRC 321:247-253
  13. Saetrom P. (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20(17):3055-3063
  14. Takasaki S, Kotani S, Konagaya A. (2004) An Effective Method for Selecting siRNA Target Seqeunces in Mammalian Cells. Cell Cycle 3(6):790-795
  15. 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
  16. Wang L, Mu FY. (2004) A Web-based design center for vector-based siRNA and siRNA cassette. Bioinformatics 20(11):1818-20.
  17. 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
  18. 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
  19. Yuan B, Latek R, Hossbach M, Tuschl T, Lewitter F. (2004) siRNA selection Server: an automated siRNA oligonucleotide prediction server. NAR 32:W130-W134
  20. Santoyo J, Vaquerizas JM, Dopazo J. (2005) Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics. 21(8):1376-82
  21. Yamada T, Morishita S. (2005) Accelerated off-target search algorithm for siRNA. Bioinformatics. 21(8):1316-24