They are specified in reverse order because ordinarily one would use the McCaldon-Argos distribution as the frequency distribution for the first sequence and tailor the frequency distribution for the second file to an individual database. The values of gamma and p are used to estimate the significance of the local alignment scores derived from comparing the sequences in db and the sequence in file2 with the scoring parameters described below. By default, direct simulation of 1000 repeated sequences is used to determine gamma and p . For this reason, we recommend simply using direct simulation with no declumping with the current software. The first line is the sequence name, and should be used as a description.
Subsequent lines contain the sequence to be used.
The sequences themselves may contain blanks, returns, and other whitespace for readability. Only multiple sequences in the first file will be processed. This allows matrices to be built for protein, DNA, and RNA sequences depending upon the letters used. The most common use of this matrix is to compare amino acid sequences in proteins, but the flexibility of the matrix input allows other types of sequences to be compared. Do not print the above-mentioned table of observed and predicted probabilities.