BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives

被引：18

作者：

Becker, Daniel ^{[1
,2
]}

Lutsik, Pavlo ^{[1
]}

Ebert, Peter ^{[2
]}

Bock, Christoph ^{[2
,3
,4
]}

Lengauer, Thomas ^{[2
]}

Walter, Joern ^{[1
]}

机构：

[1] Univ Saarland, Dept Genet, D-66123 Saarbrucken, Germany

[2] Max Planck Inst Informat, Dept Computat Biol & Appl Algorithms, D-66123 Saarbrucken, Germany

[3] Austrian Acad Sci, CeMM Res Ctr Mol Med, A-1090 Vienna, Austria

[4] Med Univ Vienna, Dept Lab Med, A-1090 Vienna, Austria

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / W1期

关键词：

DNA METHYLATION; 5-HYDROXYMETHYLCYTOSINE; DEMETHYLATION; DYNAMICS; ROLES; TDG; TET;

D O I：

10.1093/nar/gku457

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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/.

引用

页码：W501 / W507

页数：7

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