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. 2011 May 27;12:214. doi: 10.1186/1471-2105-12-214

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Copyright ©2011 Meyer et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Unidirectional (left) and bidirectional (right) searches for the RNA sequence-structure pattern (RSSP) with P = NNNUGCUNNN and R = (((....))), which represents a stem-loop structure of length m = 10. The numbers indicate the order in which the pattern characters are matched against the target sequence. In the unidirectional search, the characters are matched in a single direction, beginning (ending) with a character in φ(P[0]) (φ(P[m - 1])). In the bidirectional search, the loop region of the pattern can be matched first. Then, pairing bases are matched consecutively by switching the search direction, represented by the red arrows.

Inline graphic — Unidirectional (left) and bidirectional (right) searches for the RNA sequence-structure pattern (RSSP) with P = NNNUGCUNNN and R = (((....))), which represents a stem-loop structure of length m = 10. The numbers indicate the order in which the pattern characters are matched against the target sequence. In the unidirectional search, the characters are matched in a single direction, beginning (ending) with a character in φ(P[0]) (φ(P[m - 1])). In the bidirectional search, the loop region of the pattern can be matched first. Then, pairing bases are matched consecutively by switching the search direction, represented by the red arrows.