The number of comparisons increases linearly in proportion to average sequence length. In contrast, the time taken in dot matrix and dynamic programming methods increases as the square of the average sequence length. The larger the k-tuple chosen, the more rapid but less thorough, a database search. The speed will be increased but the sensitivity decreased as the n-mer length is increased. The process can be speeded up by compressing the DNA sequences into a more compact binary form.
Older versions are less suitable.
Fasta3 uses the extreme value distribution to calculate the significance of similarity scores found in a database search. Fasta plots a distribution of the scores found and show how well the scores with unrelated sequences match the extreme value distribution. Thus an alignment score with a standard deviation of 5 has a normalized score of 100. Pearson recommends repeating the search with a higher gap penalty if the scores do not match the expected distribution very well. Amino acid substitution matrices from protein blocks.