Automatic estimation of mobility shift coefficients in DNA chromatograms

A physical understanding of mobility pattern differences among DNA fragments of different length drives the formulation of a complete statistical model for mobility shifts correction (MSC). Algorithms are then developed that compute mobility shifts and correct the raw trace, leaving significant peaks aligned i.e. in correct order and centered with respect to their neighbors. The fully automated MSC method we develop is shown to improve substantially base-calling performance in the first 100-200 bp of DNA sequencing reads while it does not require any dye chemistry specific calibration procedure. This is very encouraging since it is known that lack of adequate MSC is the main source of base-calling errors in the early part of a DNA sequencing read.