RNAit is a tool to facilitate the accurate design of RNAi
constructs for typanosomes. Primer3 is used to identify potential
primer pairs for creation of RNAi constructs, and the resulting
products of these primer pairs are then screened against a blast
databases of CDS sequences from the target organism to identify
potentially conflicting sequences. Sequences which have >89%
identity, or stretches of >20bp of identical bases have been
identified as likely candidates for co-suppression.
Blast hits are placed in three categories as follows:
| Self match | Sequence identity > 99%; Alignment length > 95% length of query sequence |
|---|
| Conflicting | Sequence identity between specified minimim and maximum values |
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| Exceeding subunit length | Hits with exact matches longer than the defined subunit length |
|---|
Primer pairs which do not have any hits classified as 'Conficting'
or 'Exceeding subunit length' are considered good candidates.
RNAit was developed by The Field
Lab. This is a reimplementation of the original system by The Data Analysis
Group
Citation: Redmond et al. 2003, Mol. Biochem.
Parasitol. 128:115-118. doi:10.1016/S0166-6851(03)00045-8
