A domain interaction map based on phylogenetic profiling

Philipp Pagel, Philip Wong, Dmitrij Frishman

Research output: Contribution to journalArticlepeer-review

70 Scopus citations


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.

Original languageEnglish
Pages (from-to)1331-1346
Number of pages16
JournalJournal of Molecular Biology
Issue number5
StatePublished - 10 Dec 2004
Externally publishedYes


  • genome analysis
  • phylogenetic profiling
  • protein domains
  • protein-protein interactions


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