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.