title: A domain interaction map based on phylogenetic profiling.
abstract: Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins. We present a new method for finding such relations based on phylogenetic profiling of conserved domains rather than proteins, avoiding computationally expensive all versus all sequence comparisons among genomes. The resulting domain interaction map (DIMA) can be explored directly or mapped to a genome of interest. We demonstrate that the performance of DIMA is comparable to that of classical phylogenetic profiling and its predictions often yield information that cannot be detected by profiling of entire protein chains. We provide a list of novel domain associations predicted by our method.
authors.affiliation: Institute for Bioinformatics, GSF-National Research Center for Environment and Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Pagel
authors.forename: Philip
authors.initials: P
authors.lastname: Wong
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
mesh_terms: D016000:Cluster Analysis; D017124:Conserved Sequence; D030562:Databases, Protein; D019277:Entropy; D016678:Genome; D023281:Genomics; D010802:Phylogeny; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results
chemical_list: D011506:Proteins