RNA-seq, the next generation sequencing platform, enables researchers to explore deep into the transcriptome of organisms, such as identifying functional non-coding RNAs (ncRNAs), and quantify their expressions on tissues. The functions of ncRNAs are mostly related to their secondary structures. Thus by exploring the clustering in terms of structural profiles of the corresponding read-segments would be essential and this fuels in our motivation behind this research. In this manuscript we proposed PR2S2Clust, Patched RNA-seq Read Segments’ Structure-oriented Clustering, which is an analysis platform to extract features to prepare the secondary structure profiles of the RNA-seq read segments. It provides a strategy to employ the profiles to annotate the segments into ncRNA classes using several clustering strategies. The system considers seven pairwise structural distance metrics by considering short-read mappings onto each structure, which we term as the “patched structure” while clustering the segments. I...
['Ashis Kumer Biswas', 'Jean Gao']
PR2S2Clust: Patched RNA-seq read segments' structure-oriented clustering.