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Nucleic Acids Research, 2003, Vol. 31, No. 1 63-67
© 2003 Oxford University Press

ParaDB: a tool for paralogy mapping in vertebrate genomes

Magalie Leveugle*,1,3, Karine Prat1,4, Nadine Perrier1, Daniel Birnbaum1,2,5 and François Coulier1,2

1 Laboratoire d'Oncologie Moléculaire, Unité 119 INSERM, Marseille, France 2 Atelier de Bioinformatique, Unité 119 INSERM, Marseille, France 3 Université de la Méditerranée, Marseille, France 4 Laboratoire de Minéralogie-Cristallographie LMCP, CNRS-UMR 7590C, Paris, France 5 Laboratoire de Biologie des Tumeurs, Institut Paoli Calmettes, Marseille, France

*To whom correspondence should be addressed at INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France. Tel: +33 491758423; Fax: +33 491260364; Email: leveugle{at}marseille.inserm.fr

ABSTRACT

We present ParaDB (http://abi.marseille.inserm.fr/paradb/), a new database for large-scale paralogy studies in vertebrate genomes. We intended to collect all information (sequence, mapping and phylogenetic data) needed to map and detect new paralogous regions, previously defined as Paralogons. The AceDB database software was used to generate graphical objects and to organize data. General data were automatically collated from public sources (Ensembl, GadFly and RefSeq). ParaDB provides access to data derived from whole genome sequences (Homo sapiens, Mus musculus and Drosophila melanogaster): cDNA and protein sequences, positional information, bibliographical links. In addition, we provide BLAST results for each protein sequence, InParanoid orthologs and ‘In-Paralogs’ data, previously established paralogy data, and, to compare vertebrates and Drosophila, orthology data.


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