GeneFizz

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

References in zbMATH (referenced in 3 articles )

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  1. Coluzzi, Barbara; Yeramian, Edouard: Numerical study of DNA denaturation with self-avoidance: pseudo-critical temperatures and finite size behaviour (2016)
  2. Peto, Myron; Grant, David M.; Shoemaker, Randy C.; Cannon, Steven B.: Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences (2010)
  3. Yeramian, Edouard; Jones, Louis: Genefizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives. (2003) ioport