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Table 2 Major parameters of the PILER-CR algorithm

From: PILER-CR: Fast and accurate identification of CRISPR repeats

Parameter Description Default
minrepeat Minimum length of a repeat. Smaller values might increase sensitivity, though repeats < 16 bases are not currently known. 16
maxrepeat Maximum length of a repeat. Larger values might increase sensitivity, though repeats > 64 bases are not currently known. Larger values may also tend to give more false positives, such as RNAs. 64
minspacer Minimum spacer length. 8
minarray Minimum number of repeats in an array. A value < 3 will give large numbers of false positives. A value > 3 might increase specificity at the expense of missing shorter arrays. 3
maxspacer Maximum spacer length. 64
minrepeatratio Repeat length ratio (see caption for definition of ratio). 0.9
minspacerratio Spacer length ratio (see caption for definition of ratio). 0.75
mincons A run of minarray repeats with at least mincons similarity is required for an array to be reported. The value is specified as fractional identity 0.0 .. 1.0, with 1.0 meaning identical sequences. Increasing this value will tend to increase specificity by reducing the number of degraded or mutated repeats reported. 0.90
  1. This table describes the most important parameters of PILER-CR algorithm. The Parameter column gives the name of the command-line option for the pilercr program. "Ratios" (minrepeatratio and minspacerratio) are defined as the ratio of the smallest to the longest, thus a value close to 1.0 requires lengths to be similar, 1.0 means identical lengths. Spacer lengths sometimes vary significantly, so the default ratio is smaller than for repeat lengths. Using a value of 1.0 for minrepeatratio or mincons is not recommended as this may lead to false negatives due to boundary mis-identification.