Plant microRNA detection using the circular code information

In this paper we present a new computational method leading to the identification of a new property in the plant microRNAs. This property which is based on the circular code information is then used to detect microRNAs in plants. The common C-3 circular code X is a set of 20 trinucleotides identified in the reading frames of both eukaryotic and prokaryotic genes allowing retrieval of any frame in genes, locally anywhere in the three frames (reading frame and its two shifted frames) and automatically with the same window length of 13 nucleotides in each frame. This code X is detected around the beginning of microRNAs. This method based only on the internal structure of genes, i.e. the circular code, allows sensible and precise microRNA site identification in precursor microRNAs with a sliding window of only 14 nucleotides. (C) 2008 Elsevier Ltd. All rights reserved.