Finding out the way to measure how good a alignment algorithm is

[xingjianleng]

After we have an alignment algorithm, we should have some ways to determine whether the alignment the good or not. For both common string representation but also graph representations.

• [x] Read this paper to have some understanding of widely used method for measuring quality of alignment.
• [x] Survey the method for judging whether a graph is good or not. Consider whether they can be applied to alignment graphs.

P.S Yu mentioned that counting the number of nodes and edges in a graph could be a possible way to determine the quality. As more nodes and edges mean more possible solutions, which is not desired

[biolinyu]

It seems that my intuition on an optimal POA might be correct. Please refer to the following paper http://web.cs.ucla.edu/~stott/bioinf/recombPOA.pdf