* Local compositional analysis has been added to help identify local regions which are enriched in a particular type of amino acid. Proteins are complex heteropolymers, so plotting the local density of each amino acid with a sliding window is very difficult to visualize and interpret. To overcome this challenge, we take a two-pronged approach: firstly, amino acids are group by physiochemical properties. Secondly, we then fit the local density noisy data to a univariate spline fit to give a smoothed description of the local density along the sequence. Combined, this allows us to generate easy-to-read plots that illustrate the local density of residues at any given location along the sequence
* The Omega patterning parameter (previously kappa_proline) is re-defined as per the manuscript by Martin & Holehouse *et al.*
* A generalized patterning parameter for considering 2 or 3 letter alphabets is provided (kappa_X), allowing users to ask general questions about sequence patterning.
* The figure generation code has been further optimized, as has code documentation
If there are sequence features you would like to see added to localCIDER please don't hesitate to get in touch - we're always looking for new features to add and to further grow localCIDER as a general purpose protein analysis framework.