title: PfamAlyzer: domain-centric homology search.
abstract: PfamAlyzer is a Java applet that enables exploration of Pfam domain architectures using a user-friendly graphical interface. It can search the UniProt protein database for a domain pattern. Domain patterns similar to the query are presented graphically by PfamAlyzer either in a ranked list or pinned to the tree of life. Such domain-centric homology search can assist identification of distant homologs with shared domain architecture.
  
  
  BACKGROUND
  PfamAlyzer has been integrated with the Pfam database and can be accessed at http://pfam.cgb.ki.se/pfamalyzer.
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Volker
authors.initials: V
authors.lastname: Hollich
authors.forename: Erik L L
authors.initials: EL
authors.lastname: Sonnhammer
mesh_terms: D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D011381:Programming Languages; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins