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Table 1 Description of the user-specified parameters for SNP and PCR-RFLP analyses

From: Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays

User Specified Parameters Description
min_len_upstream minimum length of conserved sequence upstream (5') of a SNP
min_len_downstream minimum length of conserved sequence downstream (3') of a SNP
max_amplicon_length maximum amplicon length allowed for PCR-RFLP analysis
jump the series of sequences input to primer3 for amplicon generation for PCR-RFLP analyses are chosen by sliding a window along the consensus gestalt. Each new window must start at least jump bases from the start of the previous window.
precision there must be at least one difference in fragment lengths among all input genomes that is at least this long for the given amplicon+enzyme combination to be considered variable enough for further PCR-RFLP examination.
num_restriction_enzymes number of restriction enzymes used in an PCR-RFLP analysis before a single electrophoretic determination of fragment length distributions is made. This number may range from 0–3.
number_combinations_to_test maximum number of haplotypes per combination tested in a multi-locus solution set to maximally discriminate all the input sequences. Thus, combinatorics are performed on number haplotypessCnumber_combinations_to_test total combinations.