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TrypanoFAN: RNAit - target selection script

This script uses MIT Primer3 and NCBI Blast for the identification of primers for production of RNAi constructs, considering oligonucleotide melting temperature and PCR product size. The program is intended to prevent cross-talk between related gene products in the design of RNAi experiments.

Please note: alteration of the selection criteria will affect the fragment which is BLASTed, and therefore may alter the prediction.

Paste your DNA sequence here
(5'→3' ascii/fasta)
or select a file to upload
(single sequences only)
blastn stringency perfect match exclusion length database
Trypanosoma brucei 927
Trypanosoma brucei 927 (old version)
Leishmania braziliensis
primer Tm PCR product size range bp → bp

This service is available as is and at your own risk. Neither the University of Cambridge nor TrypanoFAN give any representation or warranty nor assume any liability or responsibility for the service or results posted.

Primer 3-1.1.1 Copyright (c) 1996,1997,1998 Whitehead Institute for Biomedical Research. All rights reserved.

Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386 (Code available at http://www-genome.wi.mit.edu/genome_software/other/primer3.html.

BLASTN 2.2.17 [Aug-26-2007]
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.

Redmond S, Vadivelu J, Field MC (2003). RNAit: an automated web-based tool for the selection of RNAi targets in Trypanosoma brucei, Mol. Biochem. Parasitol. 128, 115–118.