Notung-DM reconstructs multidomain evolution!  

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  • For gene tree - species tree reconciliation, please go to Notung 2.9

     Notung-DM is a beta release and may be buggy.


Notung-DM is a reconciliation engine for inferring the domain events that drive the evolution of multidomain protein families.   Multidomain proteins are mosaics of sequence fragments that encode protein modules: structural or functional units called domains.

In Notung-DM, protein evolution is modeled on three levels of organization: a domain tree evolving within a gene tree, which in turn is evolving within a species tree.   By comparing domain, gene, and species trees, Notung-DM infers the domain events

  • domain insertion within the same genome
  • domain transfer between different genomes
  • internal domain duplication
  • domain loss

that gave rise to present-day proteins.   These histories reveal the correspondence between domain architecture evolution and gene and species evolution and can be used to reconstruct the ancestral domain architectures.

Reconstructing the history of domain events has crucial consequences for predicting protein function, because gain, loss, or replacement of a domain that encodes specificity can result in an immediate and dramatic change to protein interactions.   Current methods like Wagner parsimony are unable to detect such domain replacements.

    Notung-DM was written by Maureen Stolzer, Han Lai, Minli Xu, and Dannie Durand. Notung-DM implements our novel, event-based framework for studying multidomain evolution by reconciling a domain tree with a gene tree, with additional information provided by the species tree [1].   Notung-DM is an extension of Notung 2.8 [2], which supports gene tree - species tree reconciliation.   The graphical user interface was constructed using the tree visualization library provided by FORESTER (version 1.92) [3].     For more information, contact mailto:notung@cs.cmu.edu

Citations

  [1]   Event inference in multidomain families with phylogenetic reconciliation.
    M. Stolzer, K. Siewert, H. Lai, M. Xu, D. Durand, 2015. BMC Bioinformatics, 16 (Suppl 14): S8

  [2]   Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary
   species trees. M. Stolzer, H. Lai, M. Xu, D. Sathaye, B. Vernot, D. Durand, 2012. Bioinformatics, 28 (18): i409-i415.

  [3]   ATV: display and manipulation of annotated phylogenetic trees.
    C.M. Zmasek & S.R. Eddy, 2001. Bioinformatics, 17:383-384.


This work was supported in part by NSF Grant DBI1262593.   Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.