Periodic proteins, characterized by the presence of multiple repeats of short sequence motifs, present unique challenges in their analysis and alignments. Especially interesting class of periodic proteins are irregular periodic proteins, where individual repeats can vary in length, sometimes considerably. We have developed a series of tools to classify regularity (or irregularity) of periodic proteins and to use such irregularity patterns to guide the multiple alignments. We present application of these tools to a group of Leucine Rich Repeat (LRR) proteins.
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