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Background  Detection of RNA structure similarities is still one of the major computational problems in the discovery of RNA functions. A case in point is the study of the new appreciated long non-coding RNAs (lncRNAs), emerging as new players involved in many cellular processes and molecular interactions. Among several mechanisms of action, some lncRNAs show specific substructures that are likely to be instrumental for their functioning. For instance, it has been reported in literature that some lncRNAs have a guiding or scaffolding role by binding chromatin-modifying protein complexes. Thus, a functionally characterized lncRNA (reference) can be used to infer the function of others that are functionally unknown (target), based on shared structural motifs.    Methods  In our previous work we presented a tool, MONSTER v1.0, able to identify structural motifs shared between two full-length RNAs. Our procedure is mainly composed of two ad-hoc developed algorithms:  nbRSSP_extractor  for characterizing the folding of an RNA sequence by means of a sequence-structure descriptor (i.e., an array of non-overlapping substructures located on the RNA sequence and coded by dot-bracket notation); and  SSD_finder , to enable an effective search engine for groups of matches (i.e., chains) common to the reference and target RNA based on a dynamic programming approach with a new score function. Here, we present an updated version of the previous one (MONSTER v1.1) accounting for the peculiar feature of lncRNAs that are not expected to have a unique fold, but appear to fluctuate among a large number of equally-stable folds. In particular, we improved our  SSD_finder  algorithm in order to take into account all the alternative equally-stable structures.    Results  We present an application of MONSTER v1.1 on lincRNAs, which are a specific class of lncRNAs located in genomic regions which do not overlap protein-coding genes. In particular, we provide reliable predictions of the shared chains between HOTAIR, ANRIL and COLDAIR. The latter are lincRNAs which interact with the same protein complexes of the Polycomb group and hence they are expected to share structural motifs.   Software availability:  the software package is provided as additional file  1  ("archive_updated.zip").

MONSTER v1.1: a tool to extract and search for RNA non-branching structures