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Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA.
Bioinformatics, 29(19):2479-81.
SUMMARY: Local opening of the DNA double helix is required in many fundamental biological processes and is, in part, controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed a program that predictsthe locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties with other available datasets. AVAILABILITY AND IMPLEMENTATION: Source codes freely available for download at http://www.cbp.ens-lyon.fr/doku.php?id=developpement:productions:logiciels:twistd na, implemented in Fortran90 and supported on any Unix-based operating system (Linux, Mac OS X).
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