title: Development and application of an algorithm to compute weighted multiple glycan alignments.
abstract: A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules.
  
  
  
  We have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis.
  
  
  
  http://www.rings.t.soka.ac.jp.
  
  
  
  kkiyoko@soka.ac.jp.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo 192-8577, Japan.
authors.forename: Masae
authors.initials: M
authors.lastname: Hosoda
authors.affiliation: Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo 192-8577, Japan.
authors.forename: Yukie
authors.initials: Y
authors.lastname: Akune
authors.affiliation: Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo 192-8577, Japan.
authors.forename: Kiyoko F
authors.initials: KF
authors.lastname: Aoki-Kinoshita
mesh_terms: D000465:Algorithms; D016208:Databases, Factual; D054794:Glycomics / Q000379:methods*; D015394:Molecular Structure; D009005:Monosaccharides; D011134:Polysaccharides / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009005:Monosaccharides; D011134:Polysaccharides