A context dependent method for comparing sequences

Document Type

Conference Proceeding

Publication Date



© Springer-Verlag Berlin Heidelberg 1994. A scoring scheme is presented to measure the similarity score between two biological sequences, where matches are weighted dependent on their context. The scheme generalizes a widely used scoring scheme. A dynamic programming algorithm is developed to compute a largest-scoring alignment of two sequences of lengths m and n in O(ran) time and O(m+n) space. Also developed is an algorithm for computing a largest-scoring local alignment between two sequences in quadratic time and linear space. Both algorithms are implemented as portable C programs. An experiment is conducted to compare protein alingments produced by the new global alignment program with ones by an existing program.

Publication Title

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)