siRNA target finder (Ambion)
What you can do:
Identify potential siRNA target sites within an mRNA sequence and then generates the sequences of the corresponding siRNAs.
Highlights:
- This tool follows the siRNA design guidelines described by Tuschl and colleagues.
- In general, scientists find that ~50% of siRNAs designed using this tool will reduce target gene expression by >50%.
- Paste your mRNA sequence into the window, choose your preferred end structure (3' TT or UU), and the program will scan your sequence for AA dinucleotides.
- A report is generated indicating the position of the AA dinucleotide, the 21 base target and the corresponding sense and antisense siRNA oligonucleotides.
- G/C content is calculated and displayed because Ambion researchers have found that siRNAs with lower G/C content (30-50%) are more active than those with higher G/C content.
- If desired, you can choose to limit your siRNA choices by maximum G/C content.
- Below each candidate target, you will find a link to perform a BLAST search on the sequence.
- BLAST settings are preset to the recommended default for short sequences and can be modified as you choose (for more information, see the Blast tutorial).
- You may elect to BLAST the entire genome, or perform a more restricted search against sequences from your target species. Choose siRNAs with fewer than 16x9617 contiguous base pairs of homology to other genes in your target cells.
Keywords:
- Small Interfering RNAs
- siRNA
- siRNA design tools
- RNA Interference
- gene silencing
- RNAi
Literature & Tutorials:
This record last updated: 05-06-2005