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Nucleic Acids Research 2005 33(Web Server Issue):W121-W125; doi:10.1093/nar/gki373
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

PhyloDome—visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets

Maria Novatchkova1,2,*, Michael Wildpaner2, Dieter Schweizer1 and Frank Eisenhaber2

1Gregor-Mendel-Institute (GMI) of the Austrian Academy of Sciences Dr Ignaz Seipel-Platz 2, A-1010 Vienna, Austria 2Research Institute of Molecular Pathology (IMP) Dr Bohr-Gasse 7, A-1030 Vienna, Austria

*To whom correspondence should be addressed at Mail Research Institute of Molecular Pathology, Dr Bohr-Gasse 7, A-1030 Vienna, Austria. Tel: +43 1 7973 0556; Fax: +43 1 7987 153; Email: novatchkova{at}imp.univie.ac.at

Received February 9, 2005. Revised March 7, 2005. Accepted March 7, 2005.

The analysis of taxonomic distribution and lineage-specific variation of domains and domain combinations is an important step in the assessment of their functional roles and potential interoperability. In the study of eukaryote sequence sets with many multi-domain proteins, it can become laborious to evaluate the phylogenetic context of the many occurring domains and their mutual relationships. PhyloDome is an answer to that problem. It provides a fast overview on the taxonomic spreading and potential interrelation of domains that are either given as a list of names and PFAM/SMART accessions or derived from a user-defined set of sequences. This taxonomic distribution analysis can be helpful in protein function and interaction assignment as the comparative study of potential Hedgehog pathway members in C.elegans shows. An implementation of PhyloDome is accessible for public use as a WWW-Service at http://mendel.imp.univie.ac.at/phylodome/. Software components are available on request.


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