Needleman-Wunsch Algorithm (cont.)
Maximum match is a function of sequence relationship and composition
Would like to know probability of obtaining result (maximum match) from a pair of random sequences
Estimate this experimentally
- form pairs of random sequences by randomly drawing one member from each set (I.e. have same composition as the real proteins)
- if the value found for the real proteins is significantly different from that for the random proteins then the difference is a function of the sequences alone and not of their composition