Table 2.

List of constraints in the fitting method available in HYDROID. (see Box 4 for parameter meaning)

Constraint type (Abbreviation)	Description
dSIGMA>=0	Peak width $\sigma$ is not allowed to decrease with increasing D, position of the peak (i.e. from the start of the gel to the end). This dramatically improves stability of the solution and prevents overfitting.
SIGMA<2*dD	Peak width σ is not allowed to exceed twice the distance between a given peak/band and the following peak (dD). Implies automatically “dSIGMA>=0”.
SIGMA=k*D+b	Peak width σ is linearly related to the position of the peak (D). This effectively establishes a linear relationship between band width and its mobility.
log(SIGMA)=P2(log(M))	Logarithm of peak width σ is proportional to the logarithm of the number of nucleotides in DNA, M, (or its molecular weight) via a second-degree polynomial. The optimal coefficients of polynomial are determined during fitting: ${\sigma }_i=e^{a*{\left(\log M_i\right)}^2+b*\log M_i+c}$
SAFA	Constraints as implemented in SAFA program 9, peak width is related to positions of neighboring peaks via${\sigma }_i={\sigma }_0+k*\frac{D_{i+1}-D_i}{2}$