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Figure 2 | BMC Bioinformatics

Figure 2

From: PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach

Figure 2

An illustrative example for the graph construction process in PicXAA-R. (A) The set of RNA sequences to be aligned. (B) The base-pairs are sorted according to their base-pairing probabilities. (C) The base alignments are sorted according to their transformed alignment probabilities. (D-K) Step 1- Structural skeleton construction: (D, E) Adding a new base-pair (x2, x5) and aligning that with its best match (y2, y4). (F, G) Adding a new base-pair (y1, y5) and aligning that with its best match (v1, v6). (H, I) Extending nodes c3 and c4 by adding the base-pair (z1, z5) to its best match (y1, y5). (J,K) Adding a new base-pair (z2, z4) and aligning that with its best match (v2, v5). (L-R) Step 2- Inserting highly probable local alignments: (L) Extending the node c3 by adding the base alignment (x1, y1). (M) Merging nodes c1 with c5 to include the base alignment (y2, z2) and merging nodes c2 with c6 to include the base alignment (x5, z4).(N) Adding a new node for the alignment (x3, y3). (O) Adding a new node for the alignment (z3, v3). (P) Merging nodes c9 and c10 to include the alignment (x3, v3). (Q) Adding a new node for the alignment (x4, v4). (R) Extending the node c3 by adding the base alignment (x6, z6). (S) The final alignment graph G, which gives us the set A in a legitimate topological ordering. (T) The alignment obtained from A.

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