Xiaoqiu Huang All Rights Reserved. Permission to use, copy, modify, and distribute this software and its documentation for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies. The GAP program computes a global alignment of two sequences without penalizing terminal gaps. It delivers the alignment in linear space, so long sequences can be aligned.
Users supply scoring parameters.
Each match automatically receives score 10. This simple scoring scheme may be used for DNA sequences. In general, users can define an alphabet of characters appearing in the sequences and a matrix that gives the substitution score for each pair of symbols in the alphabet. The alphabet and matrix are given in a file, where the first line lists the characters in the alphabet and the lower triangle of the matrix comes next. This general scoring scheme is useful for protein sequences where the set of protein characters and Dayhoff matrix are specified in the file.