Skip to main content
Figure 1 | BMC Bioinformatics

Figure 1

From: Efficient alignment of RNA secondary structures using sparse dynamic programming

Figure 1

Comparison between the tree-based alignment approach and the general edit-distance alignment approach in handling mis-predicted base pairs. (a) The tree-based alignment algorithm in handling mis-predicted base pairs. Row 1: The arcs on the sequences indicate the base pairs (solid arc indicates real base pairs, while dashed arc indicates mis-predicted base pairs). The structure regions indicated by the boxes are being aligned. Row 2: The two RNA structures are modeled into trees according to RNAforester[21]. The ‘P’ node was introduced to represent a base pair. Row 3: Either the bond breaking or the base-pair deletion operation is taken. The blue boxes indicate the aligned nucleotides in the bond-breaking case. The red box indicates the base pair (including its nucleotides) being deleted in the base-pair deletion case. Row 4: The corresponding alignments resulted from both operations. The boxes in the alignments correspond to those in the RNA structure trees. Neither of the alignments is correct. (b) The general edit-distance alignment algorithm in handling mis-predicted base pairs. Row 1: The same RNA structures are being aligned. Row 2: The base-pair interaction is deleted (red cross), leaving two free nucleotides. Row 3: The sequence similarity between the boxed regions is assessed using a traditional sequence alignment algorithm [28]. Row 4: The corresponding alignment is generated correctly. The boxes correspond to nucleotides that form the mis-predicted base pair.

Back to article page