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
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