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Figure 3 | BMC Bioinformatics

Figure 3

From: Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

Figure 3

Final output: web page from Seq4SNPs after processing one SNP, showing report. (1) Link to file containing the formatted, linear assay sequence (not shown, as Table 1 legend). (2) Link to the fasta file (not shown, 50 nucleotides per line). (3) Report of SNPs for this assay, showing rs number, chromosome and name (if given): for each adjacent/assay SNP: (4) rs with link to dbSNP (NCBI); (5) chromosome position (and relative position in the assay sequence, numbered 1 – 401); (6) allele, IUPAC code for the allele and 21 nucleotide sequence; validation, heterozygosity and standard error. (7) Flag indicating how SNP sequences were matched, indicating that both adjacent and assay SNP sequences were reversed. Flags indicate complications in sequence matching, reporting both of the sequences which it attempted to match. (8) When a single SNP is requested, the assay sequence sequence is shown in a format useful for checking positions. (9) GC content is given.

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