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Nucleic Acids Research 2006 34(Web Server issue):W104-W109; doi:10.1093/nar/gkl171
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

Blaise T. F. Alako1,2, Daphne Rainey3, Harm Nijveen1 and Jack A. M. Leunissen1,*

1 Laboratory of Bioinformatics, Wageningen University and Research Centre PO Box 8128, 6700 ET Wageningen, The Netherlands 2 Centre for BioSystems Genomics PO Box 98, 6700 AB Wageningen, The Netherlands 3 KEYGENE NV PO Box 216 6700 AE Wageningen, The Netherlands

*To whom correspondence should be addressed. Tel: +31 317 482 036; Fax: +31 317 483 584; Email: jack.leunissen{at}wur.nl

Received February 14, 2006. Revised March 20, 2006. Accepted March 20, 2006.

Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics problem. We present TreeDomViewer, a visualization tool available as a web-based interface that combines phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences and generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. Thereby it makes use of existing domain prediction tools such as InterProScan. TreeDomViewer adopts an evolutionary perspective on how domain structure of two or more sequences can be aligned and compared, to subsequently infer the function of an unknown homolog. This provides insight into the function assignment of, in terms of amino acid substitution, very divergent but yet closely related family members. Our tool produces an interactive scalar vector graphics image that provides orthological relationship and domain content of proteins of interest at one glance. In addition, PDF, JPEG or PNG formatted output is also provided. These features make TreeDomViewer a valuable addition to the annotation pipeline of unknown genes or gene products. TreeDomViewer is available at http://www.bioinformatics.nl/tools/treedom/.


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