The present invention relates to a method for determining size of biomolecules separated in a medium by an electric field using marker molecules of known size, comprising —(101) detecting a plurality of bands and forming a detected marker sequence and a detected unknown sequence based on a separation criterion, —(102) determining band properties for each detected band, —(103) comparing the band properties of the detected bands of the detected marker sequence with known band properties for a plurality of marker molecules forming a known marker sequence and assigning a score to each comparison, said score being based on at least one of relative distance, relative intensity, expected distance and expected intensity between bands, —(104) selecting the comparison with the highest score and associating all or a subset of the detected bands of the detected marker sequence with said plurality of marker molecules of the known marker sequence in accordance with said comparison to determine size of the all or a subset of the detected marker sequence, and —(105) comparing the bands of the detected marker sequence with the bands of the detected unknown sequence to determine a size of biomolecules for each identified band of the detected unknown sequence based on the known sizes of the marker molecules. The invention also relates to software configured to perform the method and to a computer readable medium for storing said software.