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. 2016 Jan 26;44(8):e77. doi: 10.1093/nar/gkw022

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© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — (A) The visualization of horizontal dependencies is a powerful tool to quickly investigate an alignment for co-dependent sites. Asp-10-containing sequences of calmodulin-dependent protein kinase II show no co-clustering at any of the other non-fully conserved positions. A strong preference for Asp-10 sequences to not have an Arg at position 5 however is visible and statistically significant (binomial test P-value 0.0053). (B) Representation of the same sequences with the pLogo software. In this version Asp-10 is ‘fixed’ (or conditioned on), also showing that there is no correlation between Asp-10 and position 5. However, the preference for avoiding Asp-5 remains hidden. The unfixed version (not shown) fails to capture the sequence motif altogether.