HYDROID specifications

Information


Unique identifier OMICS_32593
Name HYDROID
Alternative name HYDroxyl-Radical fOotprinting Interpretation for DNA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Other
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alexey Shaytan

Publication for HYDroxyl-Radical fOotprinting Interpretation for DNA

HYDROID citation

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Hydroxyl radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning

2017
Nucleic Acids Res
PMCID: 5765820
PMID: 28934480
DOI: 10.1093/nar/gkx616

[…] and data averaging across the lane width as implemented in ImageJ.The lane intensity profiles corresponding to hydroxyl-radical experiments were further analyzed with the help of our newly developed HYDROID Python package (available at https://github.com/ncbi/HYDROID) (publication in preparation) in order to obtain values of DNA cleavage intensities at every position in DNA sequence. Although our […]

HYDROID institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Physics, Lomonosov Moscow State University, Moscow, Russia; Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Fox Chase Cancer Center, Philadelphia, PA, USA
HYDROID funding source(s)
Supported by the Intramural Research Programs of the National Library of Medicine, the National Cancer Institute, the National Institutes of Health, the Russian Science Foundation (grant no. 14-24-00031; agreement no. 14-24-00031-p); the Howard Hughes Medical Institute Janelia Research Campus, a Johns Hopkins University Bloomberg Distinguished Professorship; the US–Russia Collaboration in the Biomedical Sciences, the National Institutes of Health Visiting Fellows program; NIH grants R01GM119398 and R21CA220151; and NIH grants R21DE025398 and P50DE019032.

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