Dev Cell, 8, 517-527. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B. and Bartel, D.P. (2002) Prediction of plant microRNA targets. Cell, 121, 207-221. Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M. and Weigel, D. (2005) Specific effects of microRNAs on the plant transcriptome. Score Free Energy Ratio (with target mimicry search) (without target mimicry search) TAPIR webserver manual The TAPIR webserver predicts targets for plant miRNAs. Two different search modes are possible, corresponding to two different tabs of the web interface.
The RNAhybrid search engine being quite slow, we have pre-computed searches for ten plant genomes and their corresponding sets of annotated miRNAs. The selected plant genomes correspond to fully sequenced genomes and for which a large set of annotated miRNAs is available. The tool is released under the terms of the GNU GPL version 2 and is free of charge for academics and nonprofit organizations. Input data Both miRNA and target sequence(s) can be pasted in text boxes as data input for the program. The default value for the cutoff is 0.7. As there is no score defined for miRNA target mimicry search, this parameter is not available. Paste microRNA sequence(s) [Fasta format] or Upload microRNA sequence(s) [Fasta format] Paste target sequence(s) [Fasta format] or Upload target sequence(s) [Fasta format] OR Pre-computed results Use precomputed results? The «Fast» mode is using the FASTA (1) search engine while the «Precise» mode is using the RNAhybrid (2) search engine.
Cell, 110, 513-520. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: tools for microRNA genomics. The results page is kept on the server for 24 hours. Mismatches, gaps and G:U pairs scores are doubled within this region.