A domain interaction map based on phylogenetic profiling.

Philipp Pagel; Philip Wong; Dmitrij Frishman

doi:10.1016/j.jmb.2004.10.019

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A domain interaction map based on phylogenetic profiling.

Philipp Pagel·Philip Wong·Dmitrij Frishman

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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.

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Cluster Analysis Conserved Sequence Databases, Protein Entropy Genome Genomics Phylogeny Protein Binding Protein Structure, Tertiary Proteins Reproducibility of Results Journal Article Research Support, Non-U.S. Gov't

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Philipp Pagel, Philip Wong, Dmitrij Frishman. 2004-12-10. A domain interaction map based on phylogenetic profiling.. https://doi.org/10.1016/j.jmb.2004.10.019

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