siRNA  DEsign
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Select the Organism Database:       Human Mouse   Enter a list of:       EMBL Ensembl Gene HUGO Locuslink PDB RefSeq UniProt/Swiss-Prot UniProt/TrEMBL     ORF target:       Discard for design  nt after START codon Discard for design  nt before STOP codon   Patterns:       AAN19TT NARN17YNN NNN19NN AAN19NN NANN17YNN AAN19 NAN19NN AARN18NN NNN19 Custom (19nt to 23nt)       Pattern filtering:       GC content:  -  % CT content:  -  % Less than  contigous Gs Less than  contigous As Less than  of the same nucleotide in a string Variation up to   % in nucleotide composition  Avoid A in position 3 [ NNAN20 ] After nt  set to  2 3 4  the minimum number of G/Cs in the next 4 bases After nt  set to  2 3 4  the minmum number of A/Ts in the next 4 bases  Avoid SNPs and Indels  Avoid exon boundaries  Avoid repeat regions  Filter oligos with less than  0 1 2 3 4 5 6 7 8 9 10  points of Reynolds et al. 2004 score  Filter oligos with a classification lower than  Ia Ib II III  based on Ui-Tei et al. 2004 classification  Filter oligos with less than  -4 -3 -2 -1 0 1 2 3 4 5 6  points of Amarzguioui & Prydz 2004 score  Filter oligos with less than  -2 -1 0 1 2 3 4  points based on Hsieh et al. 2004 paper  Filter oligos with less than  -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  points of Takasaki et al. 2004 score   BLAST filtering:       Allow inespecific BLAST alignments with   1 2 3 4 5 6 7 8 9 10  or more non-identical bases (gap)  BLAST alignments specific of Transcript   OUTPUT:       Sort by:  1. Differential Tm 2. Tm 3. Gap 4. Reynolds et al. 2004 5. Ui-Tei et al. 2004 6. Amarzguioui & Prydz 2004 7. Hsieh et al. 2004 8. Takasaki et al. 2004 Remove first 2 nt at 5' on Sense and last 2 nt at 3' on Antisense Remove first 2 nt at 5' on Sense and Antisense Remove last 2 nt at 3' on Sense and Antisense

Reference: Santoyo, J., Vaquerizas, J.M. & Dopazo, J. 2005 Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics, 21(8), 1376-1382.

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