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Bioinformatics, Vol 14, 326-331, Copyright © 1998 by Oxford University Press

ARTICLES

DIAMOD: display and modeling of DNA bending

M Dlakic and RE Harrington
Department of Biochemistry 330, University of Nevada at Reno, Reno, NV 89557-0014, USA. mensur@umich.edu

MOTIVATION: DIAMOD (Displayandmodeling ofDNA) was created as a user- friendly software for exploring and better understanding DNA structural variations, particularly DNA bending. It was intended to be as open as possible so that any of the existing or future predictive models can be used with it. RESULTS: DIAMOD features graphic display and interactive manipulation of DNA molecules on the screen. Since it works with di-, tri- or tetranucleotide models supplied as external files of angular parameters, it was recently used to evaluate critically all available predictive models for DNA bending. The program has a unique option to insert bends at defined positions in DNA sequence independently of the currently used model, which enables the simulation of both intrinsic and protein-induced kinking. Finally, many output file formats facilitate the sharing of data with other programs and the creation of visually pleasing images. AVAILABILITY: The program is available on request to academic users free of charge. It will be distributed via the WWW (http://www-personal.umich.edu/ mensur/software.html). Users with no network access can get a copy directly from the author. CONTACT: mensur@umich.edu
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