The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a threshold value. The onset of detection is a critical phase transition viewed as a localization-delocalization transition. The fidelity of the alignment is the order parameter of that transition; it leads to criteria to select optimal alignment parameters.

• Received 9 November 1995

DOI:https://doi.org/10.1103/PhysRevLett.76.2591