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Parameters
Parameter Name | Variable | Default Value | Parameter Range | Description |
|---|---|---|---|---|
FRAG_UR_D0 | 1 | >0 | minimum length of fragments produced by hydrolysis | |
FRAG_UR_DELTA | NaN1 | geometry of the fragmentation process (1=linear, 2=surface-diameter, 3=volume-diameter, etc.); if not explicitly specified (NaN), the geometry of breakage depends logarithmically on the molecule length | ||
FRAG_UR_ETA | NaN1 | intensity of fragmentation, determining the number of breaks per unit length; if not explicitly specified (NaN), is determined by the corresponding value and an expectation of 200nt (or the mean filtered fragment size, if size selection is used) long fragments |
1 NaN stands for "Not a Number" and marks the uninitialized state of a parameter
Algorithm
Frequencies of fragment sizes produced by a uniform random fragmentation process have demonstrated to fall along Weibull distributions , if the fragmentation thermodynamics depends on the molecule size:
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