ALN_TO_PROF -- convert alignment to profile format

CLEAN_SEQUENCES = <logical:1>

on

whether or not clean non-standard residues

Description:

This command will convert the alignment, currently in memory, into the profile format. For more details on the profile format, see READ_PROFILE.

If CLEAN_SEQUENCES is set to 'on', then the non-standard residues in the sequences will be cleaned before transferring into the profile format. Specifically, ASX (B) will be replaced with ASN (N), GLX (Z) will be replaced with GLN (Q) and UNK (X) will be replaced with ALA (A).

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'