Normalized global alignment for protein sequences.

Global alignment is used to compare proteins in different fields, for example in phylogenetic research. In order to reduce the length and composition dependence of global alignment scores, Z-score is computed with a Monte-Carlo algorithm. This technique requires a great number of sequence alignments on shuffled sequences, leading to a high computational cost. In this work, a normalized global alignment score is introduced in order to correct the length dependence of global alignments. This score is defined as the best ratio between the score of an alignment and its length, and an algorithm to compute it based on fractional programming is implemented. The properties and effectiveness of normalized global alignment applied to protein comparison are analyzed.