ICM Web: the interactive chromatin modeling web server.

Richard C Stolz, Thomas C Bishop

Department of Biostatistics, Tulane University, 1440 Canal Street, Suite 2001, New Orleans, LA 70112, USA.

Nucleic acids research 2010 Jul

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The interactive chromatin modeling web server (ICM Web) is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates. ICM Web takes a sequence composed of As, Cs, Gs, and Ts as input and generates (i) a nucleosome energy level diagram, (ii) coarse-grained representations of free DNA and chromatin and (iii) plots of the helical parameters (Tilt, Roll, Twist, Shift, Slide and Rise) as a function of position. The user can select from several different energy models, nucleosome structures and methods for placing nucleosomes in the energy landscape. Alternatively, if nucleosome footprints are known from experiment, ICM Web can use these positions to create a nucleosome array. The default energy model achieves a correlation coefficient of 0.7 with 100 experimentally determined values of stability and properly predicts the location of six positioned nucleosomes in the mouse mammary tumor virus (MMTV) promoter. ICM Web is suitable for interactively investigating nucleosome stability and chromatin folding for sequences up to tens of kilobases in length. No login is required to use ICM Web.

Citation

Richard C Stolz, Thomas C Bishop. ICM Web: the interactive chromatin modeling web server. Nucleic acids research. 2010 Jul;38(Web Server issue):W254-61