title: SplitTester: software to identify domains responsible for functional divergence in protein family.
abstract: BACKGROUND
  Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For the protein families with known functional subtypes (a functional split), we developed the software, SplitTester, to identify potential regions that are responsible for the observed distinct functional subtypes within the same protein family.
  
  
  RESULTS
  Our software, SplitTester, takes a multiple protein sequences alignment as input, generated from protein members of two subgroups with known functional divergence. SplitTester was designed to construct the neighbor joining tree (a split cluster) from variable-sized sliding windows across the alignment in a process called split-clustering. SplitTester identifies the regions, whose split cluster is consistent with the functional split, but may be inconsistent with the phylogeny of the protein family. We hypothesize that at least some number of these identified regions, which are not following a random mutation process, are responsible for the observed functional split. To test our method, we used reverse transcriptase from a group of Pseudoviridae retrotransposons: to identify residues specific for diverged primer recognition. Candidate regions were then mapped onto the three dimensional structures of reverse transcriptase. The locations of these amino acids within the enzyme are consistent with their biological roles.
  
  
  CONCLUSIONS
  SplitTester aims to identify specific domain sequences responsible for functional divergence of subgroups within a protein family. From the analysis of retroelements reverse transcriptase family, we successfully identified the regions splitting this family according to the primer specificity, implying their functions in the specific primer selection.
authors.affiliation: Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa 50011, USA. gaoxiang@iastate.edu
authors.forename: Xiang
authors.initials: X
authors.lastname: Gao
authors.forename: Kent A
authors.initials: KA
authors.lastname: Vander Velden
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Voytas
authors.forename: Xun
authors.initials: X
authors.lastname: Gu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D017931:DNA Primers / Q000737:chemistry; D030562:Databases, Protein; D019143:Evolution, Molecular; D020440:Gene Duplication; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011381:Programming Languages; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry; D018626:Retroelements / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D017931:DNA Primers; D011506:Proteins; D018626:Retroelements; D012194:RNA-Directed DNA Polymerase