Motivation:
Mitochondrial single nucleotide polymorphism (mtSNP) is important for clarifying the human diseases and cancers. Although some mtDNA databases are reported, a great challenge is how to provide the complete and convenient mtSNP information in the association study. In this database, we prepare the ready-to-use genotyping information for restriction fragment of length polymorphism (RFLP) to all mtSNPs in interactive and visualized manner for input and output. In addition, we provide a novel tool for mtBLAST to compensate the problem for NCBI BLAST to mtDNA.

Result:
We present a web-based database, V-MitoSNP, to provide the complete mtSNP information for (i) genome graph clicking, (ii) keyword searching by locus, disease and mtSNP rs# ID, (iii) nucleotide range clicking and (iv) gene-targeted mtBLAST by sequences. The restriction enzymes and primers for natural and mismatched PCR-RFLP and their virtual electrophoresis for all mtSNPs are provided and confirmed by true gel electrophoresis tested. Therefore, the V-MitoSNP provides the complete visualization interface for human mtSNPs association studies.

Statistics for mtSNPs:

Supplementary Fig. 1.The mtSNP primer validation for V-MitoSNP. To validate the designed primers in V-MitoSNP, the corresponding natural and/or mismatched primers for mtSNPs at position 8993, 5973, 7080, 12372, 15508, and 8829 of rCRS are tested by PCR. Lane 1, 4, 7, 10, 13, and 16 is 100bp DNA marker. The brightest band is 500bp and the band in bottom is 100bp. Primer sets for 8993, 5973 and 7080 are natural primers which are shown in duplicate at lane 2/3, lane 5/6, and lane 8/9, while for 12372, 15508, and 8829 are mismatched primers which are shown in duplicate at lane 11/12, lane 14/15 and lane 17/18, respectively.Detail PCR information is provided on line by range input.PCR was performed with the following protocol: 94°C (1 min); 4 cycles of 94°C (15s), 64°C (15 s), 70°C (15 s); 4 cycles of 94°C (15 s), 61°C (15 s), 70°C (15 s); 4 cycles of 94°C (15 s), 58°C (15 s), 70°C (15 s); 60 cycles of 94°C for (15 s), 55°C (15 s), 70°C (15 s); 94°C (1 min) and 60°C (5 min). The PCR results are confirmed by 1.5% agarose electrophoresis.