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 GTA program computes an optimal global alignment of three sequences using dynamic programming and divide-conquer techniques. The program takes cubic time and quadratic space. Note that the space requirement of the GTA program is one order of magnitude less than that of previous programs based on rigorous dynamic programming algorithms. Thus, the GTA program can be used to align three protein sequences of a few thousand residues on workstations with tens of megabytes of memory.
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.