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Figure 3 | BMC Genomics

Figure 3

From: SNP-RFLPing: restriction enzyme mining for SNPs in genomes

Figure 3

Output items for RFLP availability and SNP related information. (A) Results of input for the gene name of HUGO. H19 (gene input in Figure 2A) is used as example. Here, only part of the SNP information is shown. The SNP ID in rs#, organism, contig-position, heterozygosity, function, protein residue, codon position, and amino acid position are shown. Each SNP in the SNP list for the input gene is shown in the order of its contig position. The system provides the partial or entire selections for SNPs. (B) Detailed information results are shown by inputting information from Figure 2B. SNP information from different species is acceptable. Each SNP-containing sequence was automatically transformed into sense and antisense strands marked with "+" and "-", respectively. After selection by the first sequence with SNP (= rs8144801), the results are shown in Figure 3C. (C) Standard results of SNP-RFLPing demonstrate detailed information of restriction enzymes and their target site in each strand if available. The system shows only the "+" (sense) strand by default. The hind "-" (antisense) strand can be shown by selection a checkbox. The alternative SNP-containing sequence is separated into two sequences marked with "0" and "1". 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. Both commercial and non-commercial restriction enzymes are divided into two parts marked with blue and red colors to represent the recognition site for endonucleases with and without degenerated nucleotides, respectively.

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