How does KCaM work?
To put it simply, KCaM utilizes efficient methodologies from bioinformatics and theoretical computer science to perform its carbohydrate chain comparisons. Because of the generally small size of carbohydrate chain structures, the thoroughness of the Smith-Waterman sequence alignment algorithm has been modified for carbohydrate chains. In addition, a known polynomial time algorithm for finding the maximum common subtree of two trees has also been combined with the alignment algorithm. The algorithm compares all monosaccharides, or sugars, in the first carbohydrate structure with all of those in the second. A mapping is generated for the children of each of these nodes to compare them. The type of comparison is determined by the options the user selects. A score is applied whenever a comparison is satisfied. Then the following set of comparisons is performed by traversing up the tree structure of the carbohydrate chain (to the nodes’ parents) and the comparison is repeated. This recursio
