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 | |
OligoEngine | |||
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 |
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