This figure shows a screenshot of MethMarker's main analysis window. From top to bottom, MethMarker displays gene annotation data for the region of interest; its genomic DNA sequence as well as the bisulfite converted sequence; automatically generated assays for the supported experimental methods (COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MSP, MethyLight and MeDIP-qPCR); DNA methylation information for the region of interest, which has been loaded into MethMarker (yellow bars correspond to unmethylated CpGs, blue bars to methylated CpGs); a statistical summary of CpG positions within the region of interest; and - at the bottom - a text field providing advice for the user. All views are highly interactive and can be adjusted to control MethMarker's behavior.
Schüffler et al. Genome Biology 2009 10:R105 doi:10.1186/gb-2009-10-10-r105