The biological function of natural non-coding RNAs (ncRNA) is tightly bound to their molecular structure. Sequence analyses such as multiple sequence alignments (MSA) are the bread and butter of bio-molecules functional analysis; however, analyzing sequence and structure simultaneously is a difficult task. In this work, we propose CARNAGE (Clustering/Alignment of RNA with Graph-network Embedding), which leverages a graph neural network encoder to imprint structural information into a sequence-like embedding; therefore, downstream sequence analyses now account implicitly for structural constraints. In contrast to the traditional "supervised" alignment approaches, we trained our network on a masking problem, independent from the alignment or clustering problem. Our method is very versatile and has shown good performances in 1) designing RNAs sequences, 2) clustering sequences, and 3) aligning multiple sequences only using the simplest Needleman and Wunsch's algorithm. Not only can this approach be readily extended to RNA tridimensional structures, but it can also be applied to proteins.