Table 2 Comparison of tools for RNAi experiments
Clone MapperWormbaseUP-TORR
Clone verificationYesNoYes
Tool for searchMpscanBLATBlast
Insert typeGenomic and cDNAAll genomicGenomic and cDNA
All predicted clone inserts correspond to current Wormbase gene modelsYesN/ANo
Flexible for match of primers to gene/transcriptYes (perfect 10 bp match at 5′ or 3′ end sufficient).N/A (uses pseudo-primers)No
Secondary targetsYesOnly sjj clonesYes
Target scoreYesNoNo
Over-predictionNoYesYes
Under-predictionNoYesYes
Batch sequence retrievalYesNoNo
Optimal clone searchYesNoNo
  • RNAi, RNA interference.