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Nucleic Acids Research, 2003, Vol. 31, No. 13 3843-3849
© 2003 Oxford University Press

GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives

Edouard Yeramian* and Louis Jones1

Unité de Bio-Informatique Structurale, URA CNRS 2185, Institut Pasteur, 75724 Paris Cedex 15, France 1 Groupe Logiciels et Banques de Données, Institut Pasteur, 75724 Paris Cedex 15, France

*To whom correspondence should be addressed. Tel: +33 1 45 68 84 58; Fax: +33 1 45 68 87 19; Email: yeramian{at}pasteur.fr

The GeneFizz (http://pbga.pasteur.fr/GeneFizz) web tool permits the direct comparison between two types of segmentations for DNA sequences (possibly annotated): the coding/non-coding segmentation associated with genomic annotations (simple genes or exons in split genes) and the physics-based structural segmentation between helix and coil domains (as provided by the classical helix-coil model). There appears to be a varying degree of coincidence for different genomes between the two types of segmentations, from almost perfect to non-relevant. Following these two extremes, GeneFizz can be used for two purposes: ab initio physics-based identification of new genes (as recently shown for Plasmodium falciparum) or the exploration of possible evolutionary signals revealed by the discrepancies observed between the two types of information.


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