title: BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data.
abstract: BACKGROUND
  Bisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However, existing tools are either not scalable well, or inadequate in providing visualization and other desirable functionalities.
  
  
  RESULTS
  In order to handle ultra large sequencing data and to provide additional functions and features, we have developed BSPAT, a fast online tool for bisulfite sequencing pattern analysis. With a user-friendly web interface, BSPAT seamlessly integrates read mapping/quality control/methylation calling with methylation pattern generation and visualization. BSPAT has the following important features: 1) instead of using multiple/pairwise sequence alignment methods, BSPAT adopts an efficient and widely used sequence mapping tool to provide fast alignment of sequence reads; 2) BSPAT summarizes and visualizes DNA methylation co-occurrence patterns at a single nucleotide level, which provide valuable information in understanding the mechanism and regulation of DNA methylation; 3) based on methylation co-occurrence patterns, BSPAT can automatically detect potential allele-specific methylation (ASM) patterns, which can greatly enhance the detection and analysis of ASM patterns; 4) by linking directly with other popular databases and tools, BSPAT allows users to perform integrative analysis of methylation patterns with other genomic features together within regions of interest.
  
  
  CONCLUSIONS
  By utilizing a real bisulfite sequencing dataset generated from prostate cancer cell lines, we have shown that BSPAT is highly efficient. It has also reported some interesting methylation co-occurrence patterns and a potential allele-specific methylation case. In conclusion, BSPAT is an efficient and convenient tool for high-throughput bisulfite sequencing data analysis that can be broadly used.
authors.affiliation: Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, 44106, Ohio, USA. jingli@cwru.edu.
authors.forename: Ke
authors.initials: K
authors.lastname: Hu
authors.affiliation: Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, 44195, Ohio, USA. jingli@cwru.edu.
authors.forename: Angela H
authors.initials: AH
authors.lastname: Ting
authors.affiliation: Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, 44106, Ohio, USA. jingli@cwru.edu.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D019175:DNA Methylation; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D011471:Prostatic Neoplasms / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite