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BEAGLE: BEAGLE is a new alignment tool exploiting a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform global and local alignments.

BEAM: BEAM discovers novel, ungapped motifs (recurring, fixed-length patterns) in your RNAs secondary structures.

Nucleos: Nucleos is a webserver for the identification of nucleotide-binding sites based on the concept of nucleotide modularity. Nucleos identifies binding sites for nucleotide modules (namely the nucleobase, the carbohydrate and the phosphate) and then combines them in order to build the complete binding sites for different types of nucleotides (e.g. ADP or FAD).

Phosfinder: Phosfinder is a bioinformatic web server for the prediction of phosphate-binding sites in protein structures.