title: Analyzing glycan-binding patterns with the ProfilePSTMM Tool.
abstract: This chapter describes the ProfilePSTMM Tool, which is available as a part of the RINGS (Resource for INformatics of Glycomes at Soka) website. It implements the probabilistic model previously described by Aoki-Kinoshita et al. (Bioinformatics 22:e25-e34, 2006). This tool computes the glycan patterns that are found within a given set of glycan structures. Thus, one application of this tool is the extraction of monosaccharide patterns (profile) of a set of glycans that bind to a particular glycan-binding protein. Such patterns could be regarded as the monosaccharides that are important for glycan recognition. The resulting profiles are displayed similarly to Sequence Logos for amino acid motifs, where for each position in the glycan, the statistical distribution of monosaccharides that are found at that position are displayed graphically. An example of the analysis of Siglec-7 is described.
authors.affiliation: Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan, kkiyoko@soka.ac.jp.
authors.forename: Kiyoko F
authors.initials: KF
authors.lastname: Aoki-Kinoshita
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D054794:Glycomics; D008390:Markov Chains; D011134:Polysaccharides / Q000378:metabolism*; D012984:Software
chemical_list: D011134:Polysaccharides