RNAi target selection for Trypanosome genomes

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Sequence Input

This field accepts fasta formatted DNA sequences for the region to be targeted
Select a fasta file containing the sequence of the region to be targeted
Please paste a sequence or select a fasta file to upload

Primer Selection

Required melting temperature of primer pair
PCR product size
Minimum size (bp)
Maximum size (bp)


Blast Parameters

Minimum similarity
Maximum similarity
Minimum length of conflicting sequence
Select organism for RNAi target design
Please select a database

About RNAit

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 matchSequence identity > 99%; Alignment length > 95% length of query sequence
ConflictingSequence identity between specified minimim and maximum values
Exceeding subunit lengthHits 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