Reference: Henschel, A., Buchholz, F., Habermann, B., NAR 32,W113-W120 (2004): DEQOR, a web-based tool for the Design and Quality Control of siRNAs. full text @ NAR

For a copy of the command-line version of Deqor for high-throughput esiRNA predictions, please contact habermann@mpi-cbg.de

We have performed genome-wide esiRNA predictions for human, mouse and rat, available at the RiDDLE database.

IMPORTANT NOTICE: in case of problems in using Deqor and for feedback, please contact habermann@mpi-cbg.de.

Enter here your sequence in FASTA or raw format (5kb is the limit):      SENSE Direction! Alternatively enter here NCBI Accession-Nr.   Genome Database H. sapiens mRNA (NCBI) H. sapiens mRNA (ENSEMBL) M. musculus mRNA (NCBI) M. musculus mRNA (ENSEMBL) R. norvegicus mRNA (NCBI) R. norvegicus mRNA (ENSEMBL) C. lupus familiaris mRNA (NCBI) C. lupus familiaris mRNA (ENSEMBL) X. tropicalis mRNA (ENSEMBL) G. gallus mRNA (NCBI) G. gallus mRNA (ENSEMBL) D. rerio mRNA (NCBI) D. rerio mRNA (ENSEMBL) D. melanogaster transcriptome (FLYBASE) D.melanogaster mRNA (ENSEMBL) A. gambiae mRNA (ENSEMBL) A. gambiae genomic (NCBI) C. elegans mRNA (ENSEMBL) Arabidopsis thaliana (UniGene) Zea mays (UniGene) Oryza sativa (UniGene)

Display Filters Show Applet - uncheck if you dont have/want Java !!! Show only windows with GC percentage between 0 % 5 % 10 % 15 % 20 % 25 % 30 % 35 % 40 % 45 % 50 % 55 % and 5 % 10 % 15 % 20 % 25 % 30 % 35 % 40 % 45 % 50 % 55 % 60 % 65 % 70 % 75 % 80 % 85 % 90 % 95 % 100 % Show only windows with less then 3 4 5 6 Guanosines in a row Show only windows with quality better then 5 10 15 20 30 Show only 5 10 20 30 40 50 100 best windows Show only Cross Silencing windows Show Cross Silenced gene links Show Blast Output of Complete Sequence

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Options

window size 16 17 18 19 20 21 22 23 24 25
Consider windows with max. 0 1 2 3 mismatch
BLAST E-value threshold for detection of original gene 0.0 1e-400 1e-350 1e-300 1e-250 1e-200 1e-150 1e-100 1e-90 1e-80 1e-70 1e-60 1e-50 1e-40 1e-30 1e-20 1e-10

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Quality Parameter Configuration

Penalty for GC below 50%
Penalty for medium sense strand preference in RISC assembly	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for strong sense strand preference in RISC assembly	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for PolyG windows	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for PolyC windows	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for PolyA windows	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for PolyT windows	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for perfect match in gene other than origin	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
Penalty for match with decentral mismatch	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Penalty for match with central mismatch	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20