The MAP program computes a multiple global alignment of sequences using iterative pairwise method. The underlying algorithm for aligning two sequences computes a best overlapping alignment bewteen two sequences without penalizing terminal gaps. In addition, long internal gaps in short sequences are not heavily penalized. So MAP is good at producing an alignment where there are long terminal or internal gaps in some sequences. The MAP program is designed in a space-efficient manner, so long sequences can be aligned.
Users supply scoring parameters.
Each match automatically receives score 10. In other words, long gaps in the short sequence are given a constant penalty. This simple scoring scheme may be used for DNA sequences. In general, users can define an alphabet of characters to appear 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.