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Illustration: The top logo is a plain sequence logo. The bottom logo includes the mutual information for the respective basepair regions. The letter ``M'' Indicates the amount of mutual information for the corresponding basepairings at that position. (Data is a from Tuerk et. al. PNAS 89, pp 6988-6992, 1992.)
J. Gorodkin, L. J. Heyer, S. Brunak and G. D. Stormo. Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., Vol. 13, no. 6 pp 583-586, 1997.
T. D. Schneider and R. M. Stephens. Sequence logos: a new way to display consensus sequences. Nucleic Acids Research, Vol. 18, no. 20, pp 6097-6100, 1990. (Also check out Tom Schneiders page.)
You can also ``click in'' your structural alignment below. The final logo in postscript can then be downloaded. You can see an example of the data format here . There are some options you should set. You are welcome to send your comments or bug reports to firstname.lastname@example.org. The values shown are defaults value. The a priori probabilities for nucleotides must be sharply greater than zero and less than one. Entering one line of probabilities result in the same background distribution to be used throughout the alignment. Alternatively enter as many lines as there are positions in the alignment, corresponding to a position wise background distribution of nucleotides. The basepair ``probabilities'' may in principle take any value, however a natural interpretation of the weighted base complementarity is as probabilities, which also controls the relative scaling between sequence information and mutual structure information. For the version here we only allow basepair probabilities for AU (UA), CG (GC), and GU (UG).