V-MitoSNP: visualization of human mitochondrial SNPs.
BACKGROUND
Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs) is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved.


METHODS
V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1) color-coded visual input by selecting genes of interest on the genome graph, (2) keyword search by locus, disease and mtSNP rs# ID, (3) visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4) sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs) flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP.


CONCLUSIONS
V-MitoSNP is a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies.
Chuang
Li-Yeh
LY
Department of Chemical Engineering, I-Shou University, 840, Taiwan. chuang@isu.edu.tw
Yang
Cheng-Hong
CH
Cheng
Yu-Huei
YH
Gu
De-Leung
DL
Chang
Phei-Lang
PL
Tsui
Ke-Hung
KH
Chang
Hsueh-Wei
HW
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D030541:Databases, Genetic; D005838:Genotype; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface
D004272:DNA, Mitochondrial