COMPARE_ALIGNMENTS -- compare two alignments

Requirements:

READ_ALIGNMENT & READ_ALIGNMENT2

Description:

This command compares two pairwise alignments read by the READ_ALIGNMENT and READ_ALIGNMENT2 commands. The alignment of the first sequence with the second sequence in ALIGNMENT is evaluated with respect to ALIGNMENT2. The numbers are not symmetric; i.e., they will change if the sequences or alignments are swapped. The output in the log file is self-explanatory.

Example:

# Example for: COMPARE_ALIGNMENTS, SEQUENCE_TO_ALI

# Compare two alignments of two proteins each. In this case, the first
# alignment is a sequence-sequence alignment and the second alignment
# is a structure-structure alignment.

# ATOM_FILES and ALIGN_CODES have to be set explicitly so that the alignment 
# file has this information (ATOM_FILES is copied to the alignment array 
# during SEQUENCE_TO_ALI):

SET OUTPUT_CONTROL = 1 1 1 1 0

# Generate and save sequence-sequence alignment:
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ALIGN_CODES = '1fas', ATOM_FILES = ALIGN_CODES
READ_MODEL FILE = '2ctx'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES '2ctx', ATOM_FILES = ALIGN_CODES
ALIGN GAP_PENALTIES_1D= -600 -400
WRITE_ALIGNMENT FILE = 'toxin-seq.ali'

# Generate and save structure-structure alignment:
ALIGN3D GAP_PENALTIES_3D=  0 2.0
WRITE_ALIGNMENT FILE = 'toxin-str.ali'

SET ADD_SEQUENCE = off

# Compare the two pairwise alignments:
READ_ALIGNMENT  FILE = 'toxin-seq.ali', ALIGN_CODES = 'all'
READ_ALIGNMENT2 FILE = 'toxin-str.ali', ALIGN_CODES2 = 'all'
COMPARE_ALIGNMENTS