Fig. 1

Overview of the LncLOOM framework. a Overview of the LncLOOM methodology. LncLOOM processes ordered lists of sequences and recovers a set of ordered motifs conserved to various depths that can be further annotated as miRNA or RBP binding sites. b Schematic diagram of graph construction and motif discovery using integer linear programming (ILP) to find long non-intersecting paths. Sequences are ordered with monotonically increasing evolutionary distance from the top layer (human). BLAST high-scoring segment pairs (HSPs) that can be used to constrain the placement of edges (see the “Methods” section) are depicted as pink and red blocks beneath each sequence. The graph is used for the construction of an ILP problem, and its solution is used for the construction of a set of long paths that correspond to conserved syntenic motifs