title: Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences.
abstract: Bioinformatics research often requires conservative analyses of a group of sequences associated with a specific biological function (e.g. transcription factor binding sites, micro RNA target sites or protein post-translational modification sites). Due to the difficulty in exploring conserved motifs on a large-scale sequence data involved with various signals, a new method, MDDLogo, is developed. MDDLogo applies maximal dependence decomposition (MDD) to cluster a group of aligned signal sequences into subgroups containing statistically significant motifs. In order to extract motifs that contain a conserved biochemical property of amino acids in protein sequences, the set of 20 amino acids is further categorized according to their physicochemical properties, e.g. hydrophobicity, charge or molecular size. MDDLogo has been demonstrated to accurately identify the kinase-specific substrate motifs in 1221 human phosphorylation sites associated with seven well-known kinase families from Phospho.ELM. Moreover, in a set of plant phosphorylation data-lacking kinase information, MDDLogo has been applied to help in the investigation of substrate motifs of potential kinases and in the improvement of the identification of plant phosphorylation sites with various substrate specificities. In this study, MDDLogo is comparable with another well-known motif discover tool, Motif-X.
  
  
  BACKGROUND
  francis@saturn.yzu.edu.tw
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan. francis@saturn.yzu.edu.tw
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
authors.forename: Zong-Qing
authors.initials: ZQ
authors.lastname: Lin
authors.forename: Sheng-Jen
authors.initials: SJ
authors.lastname: Hsieh
authors.forename: Neil Arvin
authors.initials: NA
authors.lastname: Bretaña
authors.forename: Cheng-Tsung
authors.initials: CT
authors.lastname: Lu
mesh_terms: D020816:Amino Acid Motifs; D016000:Cluster Analysis; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D010766:Phosphorylation; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism; D010944:Plants / Q000737:chemistry / Q000378:metabolism; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D021382:Protein Sorting Signals; D013379:Substrate Specificity
chemical_list: D010940:Plant Proteins; D021382:Protein Sorting Signals; D011494:Protein Kinases