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Comment: fixed latex errors

Parameters

Parameter

Name

Variable

Default

Value

Parameter

Range

Description
FRAG_UR_D0
 1>0minimum length of fragments produced by hydrolysis
FRAG_UR_DELTA
 NaN1geometry 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
 NaN1intensity of fragmentation, determining the number of breaks per unit length; if not explicitly specified (NaN),  is determined by the corresponding 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:

...

The Flux Simulator uses a 3-step algorithm to tokenize a molecule; first, geometry  and the number  of fragments that are obtained from the molecule are determined. We found empirically that parameter d depends logarithmically on on , the length of the molecule that is fragmented . The number of fragments produced from a specific RNA molecule is determined by , where  is the expectancy of the most abundant fragment size, computed from h and the gamma-function  of :

Second,  breakpoints are sampled uniformly from the interval [0;1[, resulting in relative length fractions  for all all  fragments. Third, relative fragment sizes  are transformed from unit space to sizes  that follow a Weibull distribution of shape d shape  by:

where  is a constant of the transformation to ensure that the sizes of the  fragments sum up exactly to the given molecule length. Latter transformation produces a slightly distorted Weibull distribution for the sizes , however the deviation is sufficiently small to be neglected in our applications.