RNA Structure Logo

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The structure logo is an extension of the sequence logo by Schneider and Stephens. We have extended the standard sequence logo to cope with any prior nucleotide distribution as well as allowing for gaps in the alignments, and indicate mutual information of basepaired positions in RNA. Thus the logo is composed by a sequence part and a structure/basepair part. The total height of the sequence information part is computed as the relative entropy between the observed fractions of a given symbol and the respective a priori probabilities, with the constraint that the a priori ``probability'' of the gap always is one. The a priori probabilities for the nucleotides sum to one. Note that this might lead to negative ``information'' if sufficiently many gaps are present at a given position. The height of each symbol can be displayed in two ways: ``type 1 logo'' where the height is proportional to its frequency, or ``type 2 logo'' where the height is in proportion to the fraction of the observed frequency and the expected (a priori) frequency. In both cases, when a symbol appears less than expected the symbol will be displayed up-side-down. The mutual information between indicated (given from the structural alignment) basepair is symmetric so each involved position do Only obtain half of the shared mutual information. The mutual information is calculated as the relative entropy between the fractions of complementary bases at indicated basepaired positions in the alignment and the number of basepairs one would expect by chance from the distribution of nucleotides at the involved positions. Also a similar page for proteins has been constructed. See the paper below for further details. You can get the scripts here or you can ``click in'' your alignment below. However the script has been written such that it is possible to use position wise background distribution. For usage of the structure logos please quote
* 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.)
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.)

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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 webmaster@rth.dk. 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).

A priori nucleotide distribution
(4 decimal precision):
Basepair weights:
prob_A; prob_C; prob_G; prob_U


Structure logo
or plain Sequence logo
Structure field assignment
or no field assignment
Logo type 1
Logo type 2

Alignment start position: Use zero in position numbering or not
Display T's rather than U's

Structure Alignment: