CpG PatternFinder: A Windows®-Based Utility Program for Easy and Rapid Identification of the CpG Methylation Status of DNA

Abstract

The bisulfite genomic sequencing technique is one of the most widely used techniques to study sequence-specific DNA methylation because of its unambiguous ability to reveal DNA methylation status to the order of a single nucleotide. One characteristic feature of the bisulfite genomic sequencing technique is that a number of sample sequence files will be produced from a single DNA sample. The PCR products of bisulfite-treated DNA samples cannot be sequenced directly because they are heterogeneous in nature; therefore they should be cloned into suitable plasmids and then sequenced. This procedure generates an enormous number of sample DNA sequence files as well as adding extra bases belonging to the plasmids to the sequence, which will cause problems in the final sequence comparison. Finding the methylation status for each CpG in each sample sequence is not an easy job. As a result CpG PatternFinder was developed for this purpose. The main functions of the CpG PatternFinder are: (i) to analyze the reference sequence to obtain CpG and non-CpG-C residue position information. (ii) To tailor sample sequence files (delete insertions and mark deletions from the sample sequence files) based on a configuration of ClustalW multiple alignment. (iii) To align sample sequence files with a reference file to obtain bisulfite conversion efficiency and CpG methylation status. And, (iv) to produce graphics, highlighted aligned sequence text and a summary report which can be easily exported to Microsoft Office suite. CpG PatternFinder is designed to operate cooperatively with BioEdit, a freeware on the internet. It can handle up to 100 files of sample DNA sequences simultaneously, and the total CpG pattern analysis process can be finished in minutes. CpG PatternFinder is an ideal software tool for DNA methylation studies to determine the differential methylation pattern in a large number of individuals in a population. Previously we developed the CpG Analyzer program; CpG PatternFinder is our further effort to create software tools for DNA methylation studies.

QUMA: quantification tool for methylation analysis

“…To align bisulfite sequences with a genomic sequence, we took a pairwise-alignment approach for QUMA, instead of the multiple-alignment approach used by some other programs (6,10,13,14). QUMA aligns a target genomic sequence with each bisulfite sequence, and therefore the alignment of a certain bisulfite sequence is independent of other bisulfite sequences.…”

“…However, it requires aligned sequences as input data, so that trimming and multiple-alignment of raw sequences are necessary prior to data submission. Similarly, CyMATE (13), a unique mapping tool for both CpG and non-CpG methylation, and CpG PatternFinder (14), a Windows-based program, also require aligned sequences as input data. MethTools and CyMATE receive input data through a web submission form and return their results by Email.…”

Methyl‐Typing: An improved and visualized COBRA software for epigenomic studies

“…MethTools [14] and CyMATE [15] are web‐based methylation analyzers for input and email output. CyMATE and CpG PatternFinder [16] require aligned sequences as input data. QUMA provides quantification for methylation analysis by bisulfite sequencing [17].…”

Methylation plotter: a web tool for dynamic visualization of DNA methylation data

“…Specialized tools have been developed to work with converted bisulfite sequence files and to explore methylation trends, but are highly dependent on the operating system: MethTools, [7]) is Unix-based, and CpG Analyzer [8] or CpG PatternFinder [9]) run under Windows. MethDB [10] offers a web tool and thus is platform-independent, but is designed as a methylation data provider rather than a graphical tool.…”