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Figure 2 | BMC Bioinformatics

Figure 2

From: V-MitoSNP: visualization of human mitochondrial SNPs

Figure 2

Graphic input and output format for V-MitoSNP. The mtSNP with corresponding SNP rs# ID in chromosome MT of NCBI dbSNP [19] is shown parallel if available. When the sequences are suitable for restriction enzymes, the RFLP result shows "V". In contrast, if no RFLP is available in the restriction enzyme, "X" is shown. (A) Gene selection for graphic input on map of the human mtDNA. (B) Graphic output for the ND5 gene. The mtSNPs without cancer and disease reports are shown by default. In the red box the choices for SNP information are shown. (C) Graphic output for disease-mtSNPs. (D) Graphic output for cancer-related mtSNPs. (E) An SNP with its corresponding flanking sequence (500 bp) is provided by clicking "show sequence" in the red box in Figure 2B. (F) Standard results of V-MitoSNP demonstrate detailed information, including RFLP available restriction enzymes, target site, ready-for-use primers (natural or mismatched), and virtual electrophoresis results. The C12815T mtSNP is selected as an example. The complementary SNP sequence is separated into two sequences marked "0" and "1", i.e. C = 0, T = 1 in C12815T. The sense and antisense strands are represented as"+" and "-", respectively. Both commercial and non-commercial restriction enzymes are divided into two parts marked with blue and red colors, which represent the recognition sites for endonucleases with and without degenerated nucleotides, respectively. Two virtual electrophoresis results are provided for sequence (+/-) = 0 and sequence (+/-) = 1.

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