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. It delivers the alignment in linear space, so long sequences can be aligned.
Users supply scoring parameters.
Each match automatically receives a score of 10. A match in a substitution block receives a single left bonus of b if at least one other match occurs within l positions to the left of the match. Similarly, a match in a substitution block receives a single right bonus of b if at least one other match occurs within l positions to the right of the match. 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 context-independent substitution score for each pair of symbols in the alphabet.