A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences

Background: The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs. The latter are involved in protein interactions and formation of regulatory complexes. The function of such proteins, which may be difficult to define, is the aggregate of the subfunctions of the modules. It is therefore desirable to efficiently predict linear motifs with some degree of accuracy, yet sequence database searches return results that are not significant. Results: We have developed a method for scoring the conservation of linear motif instances. It requires only primary sequence-derived information (e.g. multiple alignment and sequence tree) and takes into account the degenerate nature of linear motif patterns. On our benchmarking, the method accurately scores 86% of the known positive instances, while distinguishing them from random matches in 78% of the cases. The conservat...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Claudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo Lopez, Toby J. Gibson
• Keywords: BMCBI 2008, Cell Regulatory Proteins, Linear Motifs, Proteins