Patent ID: 7788043

Claim:
A process for obtaining data associated with an alignment between at least two data strings having a plurality of positions in the data strings, comprising: using a computer, automatically determining at least one characteristic of an alignment between the data strings using a particular function, the particular function facilitating an evaluation of gaps between the strings in the alignment based on a piecewise-linear non-affine gap-penalty function, wherein the gap-penalty function is a piecewise-linear function defined by: w ⁢ ⁢ w ⁡ ( i ) = w ⁢ ⁢ o + [ w ⁢ ⁢ c p ~ ⁡ ( i - k p ~ - 1 ) ] + ∑ u = 1 p ~ - 1 ⁢ [ w ⁢ ⁢ c u ⁡ ( k u - k u - 1 ) ] wherein i is a value such that k {tilde over (p)}-1 <i≦k {tilde over (p)} , ww(i), wherein the function has a y-intercept of wo, and slopes of linear functions in successive intervals are wc 1 , wc 2 , . . . , wc p , wherein the x-values at which one of the intervals ends and a next of the intervals begins are denoted k 1 , k 2 , . . . , k p-1 , wherein k u is the x-value where the u th linear function of slope wc u ends, where k 0 =0, and wherein p th function of slope wc p extends off into infinity; determining the alignment with a computation time that is proportional to products of lengths of the data strings, the alignment being determined using space that is proportional to a sum of the lengths of the data strings; and at least one of displaying or storing the data in a storage arrangement in at least one of a user-accessible format or a user-readable format.