title: TreeDom: a graphical web tool for analysing domain architecture evolution.
abstract: We present TreeDom, a web tool for graphically analysing the evolutionary history of domains in multi-domain proteins. Individual domains on the same protein chain may have distinct evolutionary histories, which is important to grasp in order to understand protein function. For instance, it may be important to know whether a domain was duplicated recently or long ago, to know the origin of inserted domains, or to know the pattern of domain loss within a protein family. TreeDom uses the Pfam database as the source of domain annotations, and displays these on a sequence tree. An advantage of TreeDom is that the user can limit the analysis to N sequences that are most similar to a query, or provide a list of sequence IDs to include. Using the Pfam alignment of the selected sequences, a tree is built and displayed together with the domain architecture of each sequence.Availablility and implementation: http://TreeDom.sbc.su.se
  
  
  
  Erik.Sonnhammer@scilifelab.se.
authors.affiliation: Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna SE-17121, Sweden FH OÖ - University of Applied Sciences Upper Austria, Hagenberg 4232, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Haider
authors.affiliation: Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna SE-17121, Sweden FH OÖ - University of Applied Sciences Upper Austria, Hagenberg 4232, Austria.
authors.forename: Marina
authors.initials: M
authors.lastname: Kavic
authors.affiliation: Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna SE-17121, Sweden.
authors.forename: Erik L L
authors.initials: EL
authors.lastname: Sonnhammer
mesh_terms: D003196:Computer Graphics; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D011506:Proteins; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins