title: JEvTrace: refinement and variations of the evolutionary trace in JAVA.
abstract: BACKGROUND
  Details of functional speciation within gene families can be difficult to identify using standard multiple sequence alignment (MSA) methods. The evolutionary trace (ET) was developed as a visualization tool to combine MSA, phylogenetic and structural data for identification of functional sites in proteins. The method has been successful in extracting evolutionary details of functional surfaces in a number of biological systems and modifications of the method are useful in creating hypotheses about the function of previously unannotated genes. We wish to facilitate the graphical interpretation of disparate data types through the creation of flexible software implementations.
  
  
  RESULTS
  We have implemented the ET method in a JAVA graphical interface, JEvTrace. Users can analyze and visualize ET input and output with respect to protein phylogeny, sequence and structure. Function discovery with JEvTrace is demonstrated on two proteins with recently determined crystal structures: YlxR from Streptococcus pneumoniae with a predicted RNA-binding function, and a Haemophilus influenzae protein of unknown function, YbaK. To facilitate analysis and storage of results we propose a MSA coloring data structure. The sequence coloring format readily captures evolutionary, biological, functional and structural features of MSAs.
  
  
  CONCLUSIONS
  Protein families and phylogeny represent complex data with statistical outliers and special cases. The JEvTrace implementation of the ET method allows detailed mining and graphical visualization of evolutionary sequence relationships.
authors.affiliation: Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94143-0450, USA.
authors.forename: Marcin P
authors.initials: MP
authors.lastname: Joachimiak
authors.forename: Fred E
authors.initials: FE
authors.lastname: Cohen
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D019757:Carbon-Oxygen Lyases; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics; D003196:Computer Graphics; D019143:Evolution, Molecular; D014644:Genetic Variation; D006193:Haemophilus influenzae / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D020836:Protein Structure, Quaternary / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D013296:Streptococcus pneumoniae / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D016601:RNA-Binding Proteins; C441638:YlxR protein, Streptococcus pneumonia; D019757:Carbon-Oxygen Lyases; C412282:HI1434 protein, Haemophilus influenzae