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- IDENTITY
- 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.
- FREQUENCY
- delete the MATRIX_FILEcommand and insert:
FREQSCORE=
The frequency of occurence of each amino acid will be used to score.
- CONSERVATION
- delete FREQSCORE and replace with CONSCORE.
- WEIGHT
- (DOdd and Egan's approach). define FREQFILE=fname where fname is
name of a file containing amino acid abundancies.
- EXPLICIT
- Write a LOOKUP file, then read this into the program
with the READ_LOOKUP=fname command.