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siRNA Design Tool

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   Intro & Info

Eurofins Genomics' siRNA design tool is a proprietary developed software designed to help you selecting the most appropriate siRNA targeting your gene(s) of interest.

The siRNA desgin tool analyses the entered DNA or RNA sequence and chooses the optimum siRNA based on the criterias described by Tuschl et al., Reynolds et al., Ui-Tei et al. and Vert Jp et al. (Please click here for more information)

By calculating the appropriate siRNA sequences, a variety of parameters for the design and the siRNA sequences are already considered and taken as default values. You either can use the default settings or modify those to customise the analysis.

Target Sequence
Copy & paste the target sequence from an external source. DNA or RNA sequence information as well as FASTA sequences ( starting with an ">" followed by the name) are possible. Line breaks and blank spaces are allowed.

Design Parameters
You can design the siRNA from the whole template (= target sequence) or limit the choices to a particular region. The mRNA motifs are the search patterns on the mRNA used to find appropriate siRNA target sites. The input is the DNA coding sequence (cds). you can choose one single motif or a mixture of all motifs (recommended).

Design Exclusion
A-,G-,C- and T- resp. U- stretches (same 3 nucleotides in a raw) are recommended to exclude from the siRNA sequence design. An RNA base at the 3' end of the siRNA sequence is also not recommended. These exclusions are already set as default for the design parameters.

siRNA Parameters
For the siRNA sequences you can define the minum and maximum GC content as well as the distance from start and stop codon.

Click on the "Design siRNA" button to get a list of appropriate siRNA sequences. The best siRNA is most likely the one that shows the highest scores. The selected siRNA sequences can directly be ordered online.

   siRNA Design

Assay Design

siRNA Name

Target Sequence


Design Parameters open / close

Coding Region (whole sequence is default)

From:

To:

mRNA motif: Info

Design Exclusion open / close
siRNA Parameters open / close
 

Minimum

Maximum

GC Content (%):

Distance from start codon:

Distance from stop codon:



* These fields are mandatory
No. siRNA Sequence (Sense) mRNA Motif start c stop c GC Dsir-Score Ui-Tei Score Reynolds Score Order

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