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HOINVGEN


NAR Molecular Biology Database Collection entry number 830
Ingo Paulsen1 and Arndt von Haeseler2,3,4,5
1Department of Bioinformatics, Institute for Computer Sciences, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
2Center for Integrative Bioinformatics Vienna, Dr Bohr-Gasse 9/6, A-1030 Vienna, Austria
3University of Vienna, Vienna, Austria
4Medical University of Vienna, Vienna, Austria
5University of Veterinary Medicine Vienna, Vienna, Austria

Database Description

INVHOGEN (INVertebrate HOmologous GENes) is a database combining the available invertebrate protein genes from UniProt (consisting of Swiss-Prot, 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 allows access to the data to evaluate homology relationships between genes and distinguish orthologous from paralogous sequences. INVHOGEN complements the well-known HOVERGEN database.

Acknowledgements

This work was supported by a grant from the Deutsche Forschungsgemeinschaft (DFG: SFB-TR1). Funding to pay the Open Access publication charges for this article was provided by the Deutsche Forschungsgemeinschaft.

References

1. Gouy,M., Gautier,C., Attimonelli,M., Lanave,C., di Paola,G. (1985) ACNUCÐa portable retrieval system for nucleic acid sequence databases: Logical and physical designs and usage. Comput. Applic. Biosci., 1, 167-172.
2. Duret,L., Perriere,G. and Gouy,M. (1999) HOVERGEN: database and software for comparative analysis of homologous vertebrate genes. In Bioinformatics and Systems, Letovsky, S. (ed.), Kluwer Academic Publishers, Boston, pp. 13-29.


Go to the abstract in the NAR 2006 Database Issue.
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