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J Mol Biol. 2004 Dec 10;344(5):1331-46.

A domain interaction map based on phylogenetic profiling.

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  • 1Institute for Bioinformatics, GSF-National Research Center for Environment and Health, Ingolst├Ądter Landstrasse 1, 85764 Neuherberg, Germany.


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.

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