Automatic extraction of hairpin sequences from genome-wide data

YONES C; STEGMAYER, G.; KAMENETZKY, L.; MILONE D.

Conferencia; IV ISCB-LA A2B2C Bioinformatics Conference; 2016

We have developed a simple and integrated tool that, relying on thelatest versions of RNAfold, automatically extracts and folds all hairpinsequences from raw genome-wide data. The method predicts the secondarystructure of several overlapped regions of the raw genome, with longer lengththan the mean for well-known pre-miRNAs of the species under processing,ensuring that no pre-miRNA is cut in the middle. Then stem-loops in theseregions that meet specified requirements are extracted and trimmed. Genomes canbe processed in parallel and it is memory efficient since it can automaticallysplit large multifasta files. It is freely available. Several genomes were processed with theproposed method and the obtained results were compared to those from mirCheck(Table 1). The number of hairpins founded were higher for the proposed method.More importantly, almost all known pre-miRNAs were found in the analyzedgenomes, both model and nonmodel species.