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GenScript siRNA Target Finder.
The availability of the large and diverse siRNA dataset from siRecords have allowed the
development of highly effective and generally applicable siRNA design
rule sets. Together with ever improving RNAi lab techniques, these
design rule sets are expected to make siRNAs a more useful tool for
molecular genetics, functional genomics, and drug discovery studies.
| List of features: |
|
| Feature Index |
Feature Names |
|
| F1 |
2nd nucleotide = A |
| F2 |
4th
nucleotide = C |
| F3 |
6th nucleotide <> C |
| F4 |
7th
nucleotide <> U |
| F5 |
9th nucleotide = C |
| F6 |
17th
nucleotide = A |
| F7 |
18th nucleotide <> C |
| F8 |
19th
nucleotide = (A/U) |
| F9 |
At least three (A/U)s in the seven
nucleotides at the 3' end |
| F10 |
No occurrences of four or more identical
nucleotides in a row |
| F11 |
No occurrences of G/C stretches of length 7
or longer |
| F12 |
G/C content is between 35 and 60% |
| F13 |
Tm
is between 20 and 60°C |
| F14 |
Binding energy of N16N19 > -9 KCal/Mol |
| F15 |
Binding
energy of N16N19 binding energy of N1N4 is between 0 and 1 KCal/Mol |
| F16 |
Local
folding potential (mean) e -22.72 KCal/Mol |
| F17 |
Target
site is on CDS |
|
Reference: Wuming Gong , Yongliang Ren , Qiqi Xu , Yejun Wang , Dong Lin , Haiyan Zhou and Tongbin Li
Integrated siRNA design based on surveying of features associated with high RNAi effectiveness Bioinformatics. , BMC Bioinformatics 2006,
7:516. |