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Nucleic Acids Research 2006 34(Database Issue):D349-D353; doi:10.1093/nar/gkj100
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Nucleic Acids Research, 2006, Vol. 34, Database issue D349-D353
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

INVHOGEN: a database of homologous invertebrate genes

Ingo Paulsen* and Arndt von Haeseler1,2,3,4

Department of Bioinformatics, Institute for Computer Sciences, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1 40225 Duesseldorf, Germany 1Center for Integrative Bioinformatics Vienna Dr Bohr-Gasse 9/6, A-1030 Vienna, Austria 2University of Vienna Vienna, Austria 3Medical University of Vienna Vienna, Austria 4University of Veterinary Medicine Vienna Vienna, Austria

*To whom correspondence should be addressed. Tel: +49 211 81 13716; Fax: +49 211 81 15767; Email: paulseni{at}uni-duesseldorf.de

Received August 15, 2005. Revised October 17, 2005. Accepted October 17, 2005.

Classification of proteins into families of homologous sequences constitutes the basis of functional analysis or of evolutionary studies. Here we present INVertebrate HOmologous GENes (INVHOGEN), a database combining the available invertebrate protein genes from UniProt (consisting of Swiss-Prot and TrEMBL) into gene families. For each family INVHOGEN provides a multiple protein alignment, a maximum likelihood based phylogenetic tree and taxonomic information about the sequences. It is possible to download the corresponding GenBank flatfiles, the alignment and the tree in Newick format. Sequences and related information have been structured in an ACNUC database under a client/server architecture. Thus, complex selections can be performed. An external graphical tool (FamFetch) allows access to the data to evaluate homology relationships between genes and distinguish orthologous from paralogous sequences. Thus, INVHOGEN complements the well-known HOVERGEN database. The databank is available at http://www.bi.uni-duesseldorf.de/~invhogen/invhogen.html.


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