Fig 1.
Workflow diagram followed to construct PeTMbase.
Raw data sets from diverse public databases were incorporated to extract the biologically relevant information. Sequence libraries were downloaded from SRA database, and known lncRNA sequences retrieved from non-coding RNA databases. MiRNA binding sites within lncRNA sequences were identified with a custom R script, and flexible and user-friendly interfaces were developed diverse scripting languages and web technologies.
Fig 2.
Illustration of an example miRNA:eTM pairing and conserved binding site.
Pairing the Z. mays miRNA, 528b-5p-19. (a) Potential binding sites of plant miRNAs were scanned within novel and known lncRNA sequences using a set of rules previously described by Wu et al[17]. (b) Several conserved miRNA binding sites were identified among eTMs. While the first eight bases (brown-colored) of target mimic site are perfectly preserved across the sequences, there are mismatches within bulge (blue-colored) and tail (green-colored) regions.
Fig 3.
An eTM:lncRNA sequence representation in PeTMbase.
The full cDNA sequence of the predicted eTMs, and their target miRNA sequences can be viewed following the database search. miRNA binding site within the eTM sequences is highlighted and the sequence properties of lncRNAs can be retrieved by clicking over the lncRNA ID.