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Figure 1 | BMC Bioinformatics

Figure 1

From: Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences

Figure 1

Correct and incorrect stem alignments. Single strand regions are generally correctly aligned because they are less variable, whereas the stem regions can be incorrectly aligned. Correct stem alignment results in an alternation between a stem substitution matrix (M H ) and a single strand substitution matrix (M S ). On the other hand, the single strand substitution matrix (M S ) alternates with another substitution matrix (M U ) different from the stem substitution matrix if stems are not correctly aligned.

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BMC Bioinformatics

ISSN: 1471-2105

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