WRITE_PROFILE -- write a profile

FILE = <string:1>	'default'	partial or complete filename
GAP_PENALTIES_1D = <real:2>	900 50	gap creation and extension penalties for sequence/sequence alignment
MATRIX_OFFSET = <real:1>	0.00	substitution matrix offset for local alignment
PROFILE_FORMAT = <string:1>	'TEXT'	'TEXT' | 'BINARY' ; for READ/WRITE_PROFILE
RR_FILE = <string:1>	'$(LIB)/as1.sim.mat'	input residue-residue scoring file

Description:

This command will write a profile to a specified file, together with a number of variables that are associated with the profile in the memory. Two formats are supported: TEXT and BINARY.

Example:

# Read in the alignment file
READ_ALIGNMENT FILE = 'toxin.ali', ALIGNMENT_FORMAT = 'PIR'

# Convert the alignment to profile format
ALN_TO_PROF CLEAN_SEQUENCES = on

# Write out the profile

# in text file
WRITE_PROFILE FILE = 'alntoprof.prf', PROFILE_FORMAT = 'TEXT'

# in binary format
WRITE_PROFILE FILE = 'alntoprof.bin', PROFILE_FORMAT = 'BINARY'