title: GlycoSiteAlign: Glycosite Alignment Based on Glycan Structure.
abstract: GlycoSiteAlign is a tool designed to align amino acid sequences of variable length surrounding glycosylation sites depending on the knowledge of glycan structure. It is an exploratory resource intended for the identification of characteristic amino acid patterns of unique glycan-protein interactions. GlycoSiteAlign uses data from the UniCarbKB and UniProtKB databases, and it is hosted on ExPASy, the Swiss Institute of Bioinformatics resource portal. The user can select either specific or general glycan features, set the length of the protein fragments, and trigger an alignment with the option of including 90% homologous proteins. The tool previews and downloads alignments that may reveal amino acid patterns corresponding to selected features (e.g., "fucosylated" versus "non-fucosylated"). GlycoSiteAlign will integrate new data as they become available to confirm and expand results. It is presented as a promising tool for assessing and refining the knowledge about the constraints that link a particular glycan structure to a particular glycosite, and in the long term, this application could help improve prediction tools.
authors: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , 7 route de Drize, 1227 Geneva, Switzerland.|Computer Science Department CUI, University of Geneva , 1227 Geneva, Switzerland.
authors: Alessandra
authors: A
authors: Gastaldello
authors: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , 7 route de Drize, 1227 Geneva, Switzerland.|Computer Science Department CUI, University of Geneva , 1227 Geneva, Switzerland.
authors: Davide
authors: D
authors: Alocci
authors: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , 7 route de Drize, 1227 Geneva, Switzerland.|Section of Biology, Faculty of Sciences, University of Geneva , 1211 Geneva, Switzerland.
authors: Jean-Luc
authors: JL
authors: Baeriswyl
authors: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , 7 route de Drize, 1227 Geneva, Switzerland.|Computer Science Department CUI, University of Geneva , 1227 Geneva, Switzerland.
authors: Julien
authors: J
authors: Mariethoz
authors: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , 7 route de Drize, 1227 Geneva, Switzerland.|Computer Science Department CUI, University of Geneva , 1227 Geneva, Switzerland.|Section of Biology, Faculty of Sciences, University of Geneva , 1211 Geneva, Switzerland.
authors: Frederique
authors: F
authors: Lisacek
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology; D030562:Databases, Protein; D006031:Glycosylation; D011134:Polysaccharides / Q000737:chemistry; D016415:Sequence Alignment; D012984:Software
chemical_list: D011134:Polysaccharides
keywords: amino acid patterns; glycan structure; glycoprotein; glycosite; glycosylation; sequence alignment