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. 2007 Mar 30;3(3):e56. doi: 10.1371/journal.pcbi.0030056

Figure 1. An Example RNA Family and Corresponding CM.

Figure 1

(A) A toy multiple alignment of three RNA sequences, with 28 total columns, 24 of which will be modeled as consensus positions. The [structure] line annotates the consensus secondary structure: angle brackets mark base pairs, colons mark consensus single-stranded positions, and periods mark “insert” columns that will not be considered part of the consensus model because more than half the sequences in these columns contain gaps.

(B) The structure of one sequence from (A), the same structure with positions numbered according to alignment columns, and the guide tree of nodes corresponding to that structure, with alignment column indices assigned to nodes (for example, node 5, a MATP match-pair node, will model the consensus base pair between columns 4 and 14).

(C) The state topology of three selected nodes of the CM, for two MATP nodes and one consensus “leftwise” single residue bulge node (MATL, “match-left”). The consensus pair and singlet states (two MPs and one ML) are white, and the insertion/deletion states are gray. State transitions are indicated by arrows.