Identifies canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter extracts peak sequences, annotates on the genome and converts miRNA sequences in Homer format by using Homer software. This pipeline works for mouse and human miRNA-mRNA pairs. miRBShunter is a valuable resource for researchers working on miRNA biology due to its easy applicability and reliability of the results.
(Bottini et al. Nucleic Acids Res. 2017)
Database of miRNA binding sites, obtained from CLIP-seq data analysis, dependent from the RNA binding protein Sfpq (Splicing Factor Proline and Glutamine Rich), that interfere with the miRNA binding activity and silencing.(Bottini et al. Nature Communications, 2017).
Comprehensive database of 106916 canonical and non canonical miRNA binding sites for 200 mIRNAs expressed in tissues and/or cell lines from human or mouse samples. These binding sites were identified from 49 datasets of Ago2 CLIP-seq using our computational pipeline “optiCLIP”.
Optimized pipeline of analysis of Ago2 CLIP-seq data obtained benchmarking several tools for each step of the data analysis and developing a new methodology to take into account replicates. It takes as input raw data after sequencing and gives as output the complete map of miRNA binding sites.
(Bottini et al. Briefings in Bioinformatics, 2017).