Frame-shifting penalty function. The figure shows the insertion and deletion penalty, P = P0- Pħ· f, Pħ = P0· (1-h), on the left y-axis as well as the gap penalty reduction factor, f, on the right y-axis for flowpeak values between 0 and 10 (x-axis). The penalties intersect at each integer peak value, noted by squares and the dotted line shows the 1/n slope of the f-function. The homopolymer length in this plot is assumed to be the integer value of the flowpeak value p (x-axis), thus p satisfies; n-0.5 ≥ p > n + 0.5, except for deletion penalties for p < 0.5 where a 1-mer is assumed.
Lysholm BMC Bioinformatics 2012 13:230 doi:10.1186/1471-2105-13-230