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Alternative scoring systems

change the matrix_file command to: MATRIX_FILE=ampsdir:UP.MAT the presence of an amino acid in an element will indicate a score of 1 with the same amino acid, 0 with all others.

delete the MATRIX_FILEcommand and insert: FREQSCORE= The frequency of occurence of each amino acid will be used to score.

delete FREQSCORE and replace with CONSCORE.

(DOdd and Egan's approach). define FREQFILE=fname where fname is name of a file containing amino acid abundancies.

Write a LOOKUP file, then read this into the program with the READ_LOOKUP=fname command.