RNA-binding protein motif enrichment software tools | RNA sequencing data analysis
RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP-RNA interactions.
Performs motif analyses of RNA-binding proteins (RBPs) in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. rMAPS is able to execute spatial analyses of RBP-RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq). It can examine RBP binding sites within endogenous RNAs identified by CLIP-seq and produce an RNA map to display the spatial distribution of binding sites for the RBP of interest.
Identifies combined sequence and structure motifs. SMARTIV associates the RNA sequence and secondary structure information in a single representation. It finds enriched k-mers that are clustered to build position weight matrices (PWMs), representing the joint sequence and structural preferences of the protein. This tool employs the minimum-minimum Hyper Geometric (mmHG) statistics approach to work.
Estimates human RNA-binding proteins. beRBP is able to determine human RNA-binding protein (RBP)-RNA interaction given position weight matrix (PWM) of an RBP and an RNA sequence. It was designed for managing any RBPs with little or no target information but known binding preferences. It embeds features for treating one or multiple RBPs/PWMs simultaneously, which is useful for screening RBP binding to RNA sequence of interest.