1. A computer system communicatively linked to a database storing single molecule image data and corresponding identifying data, the computer system programmed to: selectively retrieve at least two single molecule image data from the database wherein each single molecule image data depicts a region of a restriction fragment and comprises at least one pixel having image and intensity level data, and wherein the single molecule image data each include at least one pixel representing an overlapping region of the same single molecule image; calculate an average intensity level for at least one of the single molecule image data retrieved from the database by averaging an intensity level of each pixel of the at least one single molecule image data; display the at least two single molecule image data retrieved from the database on a user interface; display the intensity level for each pixel of the at least two single molecule image data retrieved from the database on the user interface; differentiate at least one restriction fragment in the single molecule image data from a background in the single molecule image data by applying an intensity level threshold analysis to each pixel of the single molecule image data; magnify each of the at least one restriction fragments for display on the user interface; form a collage by aligning the overlapping regions of the at least two single molecule image data; generate a linear representation of the restriction fragments by: (a) receiving an input signal from a marking tool provided to a user, the input signal indicating a point on the user interface associated with a pixel of the single molecule image data; (b) repeating step (a) to define successive points in a single restriction fragment; (c) retrieving the single molecule image data associated with points between each successive point; and (d) storing the retrieved single molecule image data as the single restriction fragment; associate the restriction fragments; order the associated restriction fragments based on their relative positions; and store the ordered restriction fragments as a restriction map in a file adapted for use in map generation.