miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction

The advent of Next Generation Sequencing (NGS) technology has enabled a new major approach for micro RNAs (miRNAs) expression profiling through the so called RNA-Sequencing (RNA-Seq). Different tools have been developed in the last years in order to detect and quantify miRNAs, especially in pathological samples, starting from the big amount of data deriving from RNA sequencing. These tools, usually relying on general purpose alignment algorithms, are however characterized by different sensitivity and accuracy levels and in the most of the cases provide not overlapping predictions. To overcome these limitations we propose a novel pipeline for miRNAs detection and quantification in RNA-Seq sample, miRNA Seed Extension Aligner (miR-SEA), based on an experimental evidence concerning miRNAs structure. The proposed pipeline was tested on three Colorectal Cancer (CRC) RNA-Seq samples and the obtained results compared with those provided by two well-known miRNAs detection tools showing good ability in performing detection and quantification more adherent to miRNAs structure.