Therefore the opt score may contain more poorly matching parts of the sequences. The lookup table indexes the position of each ktup, or word, in each sequence being compared. The lookup tables for the query and database sequence can be compared in time proportional to the number of common words in the sequences, rather than the n 2 time required for a windowed comparison. Ktup is the length of the word used in constructing the lookup table. Appropriate values for w have been empirically decided by the authors of the program.
Fractional values are acceptable.
For each of these two total sequences, calculate the Complexity Kw. The complexity of the most complex word depends on its length. Calculate how many bits of information there are in the number 100. A bit of information is the amount of information needed to distinguish between two possibilities. The PIR protein database now contains about 65 million amino acids.