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Polyadenylation plays a decisive role in the life cycle of mRNA in eukaryotic cells. The primary sequences of cis-elements of plant poly(A) sites are much less conserved than those of animal sites. The secondary structure of RNA sequences tends to be more conserved than the primary sequence and is closely related to the function of mRNA, therefore it is necessary to investigate whether there is potential secondary structures around plant poly(A) sites. Here we proposed a pipeline to characterize secondary structures surrounding plant poly(A) sites. First, poly(A) sequences of Arabidopsis were converted into the secondary structure form represented by dot-bracket notation, which is then denoted by a position number matrix and converted into a triple structure. The triple structure is based on the structure of the stem region, on which each structural unit of the secondary structure is described. Each structural unit has a corresponding mathematical model that is used to determine various structures of the sequence. Finally, the size and position of secondary structures surrounding poly(A) sites are obtained. Using this pipeline, we provided a detailed view of the secondary structure of plant poly(A) regions, which help understand the functional importance of plant poly(A) signals and associated secondary structures.
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