RBPmap: a web server for mapping binding sites of RNA-binding proteins.
Paz et al., Nucleic Acids Res., 2014.

BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins

DRIMust: a web server for Discovering Rank Imbalanced Motifs Using Suffix Trees.
Leibovich et al., Nucleic Acids Res., 2013.

Sequence & Structure Motif Enrichment Analysis for Ranked RNA Data from In-Vivo Binding Experiments.Polishchuk et al., Methods, 2017.

The algorithm outputs a list of structures, each composed of a group of genes working simultaneously in a specific population of cells.