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

摘要

The GeneFizz (http://pbga.pasteur.fr/GeneFizz) web tool permits the direct comparison between two types of segmentations for DNA sequences (possibly annotated): the codingon-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.