title: BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.
abstract: Recent data suggest important biological roles for oxidative modifications of methylated cytosines, specifically hydroxymethylation, formylation and carboxylation. Several assays are now available for profiling these DNA modifications genome-wide as well as in targeted, locus-specific settings. Here we present BiQ Analyzer HiMod, a user-friendly software tool for sequence alignment, quality control and initial analysis of locus-specific DNA modification data. The software supports four different assay types, and it leads the user from raw sequence reads to DNA modification statistics and publication-quality plots. BiQ Analyzer HiMod combines well-established graphical user interface of its predecessor tool, BiQ Analyzer HT, with new and extended analysis modes. BiQ Analyzer HiMod also includes updates of the analysis workspace, an intuitive interface, a custom vector graphics engine and support of additional input and output data formats. The tool is freely available as a stand-alone installation package from http://biq-analyzer-himod.bioinf.mpi-inf.mpg.de/.
authors.affiliation: Department of Genetics, Saarland University, Saarbrücken 66123, Germany Department of Computational Biology and Applied Algorithms, Max-Planck Institute for Informatics, Saarbrücken 66123, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Becker
authors.affiliation: Department of Genetics, Saarland University, Saarbrücken 66123, Germany p.lutsik@mx.uni-saarland.de.
authors.forename: Pavlo
authors.initials: P
authors.lastname: Lutsik
authors.affiliation: Department of Computational Biology and Applied Algorithms, Max-Planck Institute for Informatics, Saarbrücken 66123, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Ebert
authors.affiliation: Department of Computational Biology and Applied Algorithms, Max-Planck Institute for Informatics, Saarbrücken 66123, Germany CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria.
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
authors.affiliation: Department of Computational Biology and Applied Algorithms, Max-Planck Institute for Informatics, Saarbrücken 66123, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
authors.affiliation: Department of Genetics, Saarland University, Saarbrücken 66123, Germany j.walter@mx.uni-saarland.de.
authors.forename: Jörn
authors.initials: J
authors.lastname: Walter
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis*; D000818:Animals; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D051379:Mice; D010084:Oxidation-Reduction; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D044503:5-Methylcytosine; D004247:DNA