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siDirect

Highly effective, target specific siRNA online design site. Or Paste in a nucleotide sequence:. Sample sequence ggctgccaag aacctgcagg aggcagaaga atggtacaaa tccaagtttg ctgacctctc tgaggctgcc aaccggaaca atgacgccct gcgccaggca aagcaggagt ccactgagta ccggagacag gtgcagtccc tcacctgtga agtggatgcc cttaaaggaa ccaatgagtc cctggaacgc cagatgcgtg aaatggaaga gaactttgcc gttgaagctg ctaactacca agacactatt ggccgcctgc aggatgagat tcagaatatg aaggaggaaa tggctcgtca ccttcgtgaa taccaagacc tgctcaatgt taagatggcc cttgacattg agattgccac c...

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siDirect | sidirect2.rnai.jp Reviews

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Highly effective, target specific siRNA online design site. Or Paste in a nucleotide sequence:. Sample sequence ggctgccaag aacctgcagg aggcagaaga atggtacaaa tccaagtttg ctgacctctc tgaggctgcc aaccggaaca atgacgccct gcgccaggca aagcaggagt ccactgagta ccggagacag gtgcagtccc tcacctgtga agtggatgcc cttaaaggaa ccaatgagtc cctggaacgc cagatgcgtg aaatggaaga gaactttgcc gttgaagctg ctaactacca agacactatt ggccgcctgc aggatgagat tcagaatatg aaggaggaaa tggctcgtca ccttcgtgaa taccaagacc tgctcaatgt taagatggcc cttgacattg agattgccac c...

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1 sidirect

2 version 2 0

3 options

4 functional sirna selection

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6 ui tei et al

7 nucleic acids res

8 reynolds et al

9 nat biotechnol

10 amarzguioui et al

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siDirect | sidirect2.rnai.jp Reviews

https://sidirect2.rnai.jp

Highly effective, target specific siRNA online design site. Or Paste in a nucleotide sequence:. Sample sequence ggctgccaag aacctgcagg aggcagaaga atggtacaaa tccaagtttg ctgacctctc tgaggctgcc aaccggaaca atgacgccct gcgccaggca aagcaggagt ccactgagta ccggagacag gtgcagtccc tcacctgtga agtggatgcc cttaaaggaa ccaatgagtc cctggaacgc cagatgcgtg aaatggaaga gaactttgcc gttgaagctg ctaactacca agacactatt ggccgcctgc aggatgagat tcagaatatg aaggaggaaa tggctcgtca ccttcgtgaa taccaagacc tgctcaatgt taagatggcc cttgacattg agattgccac c...

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sidirect2.rnai.jp

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siDirect

http://sidirect2.rnai.jp/doc/NRDB.html

Specificity check using non-redundant database of mRNA sequences. Several studies show that single base mismatch between the siRNA guide strand and the target mRNA is permissible to induce target mRNA cleavage ( Du et al. 2005; Birmingham et al. Accordingly, siDirect avoids off-target hits with less than three mismatches by exhaustively searching the non-redundant database of mRNA sequences. Overview of non-redundant database of mRNA sequences. See the referece ( Naito et al.

2

siDirect

http://sidirect2.rnai.jp/doc/algorithms.html

Selection of highly functional siRNAs. 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. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. (2004). Rational siRNA design for RNA interference. Amarzguioui M, Prydz H. (2004). An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun. Gene as a reporter.

3

siDirect

http://sidirect2.rnai.jp/doc

About siDirect 2.0. SiDirect 2.0 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 ( reference 6. Example 1 Designing siRNAs for human claudin 17 (CLDN17). And Amarzguioui et al. Graph...

4

siDirect

http://sidirect2.rnai.jp/doc/seedTm.html

Minimization of seed-dependent off-target effects. SiDirect selects siRNAs with lower Tm value at the seed. Region, which contains 7 nucleotides at positions 2-8 from 5′ end of the guide strand. The figure above shows correlation between seed-dependent off-target activity and seed Tm value. All possible 7-nt seed sequences (4 7 = 16,384) were ordered as a function of GC content and Tm. Blue:. Pairs of target and siRNA, giving significant off-target effects. Red:.

5

siDirect

http://sidirect2.rnai.jp/doc/pattern.html

Custom pattern / Exclude pattern. Write custom pattern / exclude pattern in IUB code. Case insensitive.

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sidirect2.rnai.jp

siDirect

Highly effective, target specific siRNA online design site. Or Paste in a nucleotide sequence:. Sample sequence ggctgccaag aacctgcagg aggcagaaga atggtacaaa tccaagtttg ctgacctctc tgaggctgcc aaccggaaca atgacgccct gcgccaggca aagcaggagt ccactgagta ccggagacag gtgcagtccc tcacctgtga agtggatgcc cttaaaggaa ccaatgagtc cctggaacgc cagatgcgtg aaatggaaga gaactttgcc gttgaagctg ctaactacca agacactatt ggccgcctgc aggatgagat tcagaatatg aaggaggaaa tggctcgtca ccttcgtgaa taccaagacc tgctcaatgt taagatggcc cttgacattg agattgccac c...

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