Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment

Additional file 1:

Graphical representations HSL3 (A) and IRE (B). The structures are also represented in the dot-bracket form.

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Additional file 2:

Heat map for all-against-all comparisons of 2,054 human RNA structures. The normalized dissimilarity score is represented by color based on the scale shown at the bottom. The structures are in the same order as those shown in the hierarchical clustering tree in Figure 3B.

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Additional file 3:

GLEAN-UTR for randomized UTR sequences. UTR sequences randomized by 1-order Markov chain were subject to the same GLEAN-UTR approach as shown in Figure 1. The numbers of structures and structure groups are shown in parenthesis.

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Additional file 4:

Structures identified both by this study and by Washietl et al. or Pedersen et al.

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Additional file 5:

Extending RNA structure groups by PatSearch. The 90 structure groups were used to search human UTRs to obtain additional group members using PatSearch. GO analysis refers to filtering out hits without the same GO term annotation as the original group. The structure groups are ordered according to the difference between the original group size and the group size after PatSearch.

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