Introduction

Bisulphite genomic sequencing is a widely used technique for detailed analysis of the methylation status of a region of DNA. It relies upon the selective deamination of unmethylated cytosine to uracil after treatment with sodium bisulphite, usually followed by PCR amplification of the chosen target region. Since this two-step procedure replaces all unmethylated cytosine bases with thymine, PCR products derived from unmethylated templates contain only three types of nucleotide, in unequal proportions. This can create a number of technical difficulties (e.g. for some base-calling methods) and impedes manual analysis of sequencing results (since the long runs of T or A residues are difficult to align visually with the parent sequence). To facilitate the detailed analysis of bisulphite PCR products (particularly using multiple cloned templates), we have developed a visually intuitive program that identifies the methylation status of CpG dinucleotides by analysis of raw sequence data files produced by MegaBace or ABI sequencers as well as Staden SCF trace files and plain text files. The program then also collates and presents data derived from independent templates (e.g. separate clones). This results in a considerable reduction in the time required for completion of a detailed genomic methylation project.

Publications

  1. Sequence analysis and editing for bisulphite genomic sequencing projects.
    Cite this
    Carr IM, Valleley EM, Cordery SF, Markham AF, Bonthron DT, 2007-01-01 - Nucleic acids research

Credits

  1. Ian M Carr
    Developer

  2. Elizabeth M A Valleley
    Developer

  3. Sarah F Cordery
    Developer

  4. Alexander F Markham
    Developer

  5. David T Bonthron
    Investigator

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Summary
AccessionBT006361
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByDavid T Bonthron