Example: aligning myoglobin sequences with an existing alignment derived from three dimensional structure superposition.
Command file: bash_mult.com
output_file=bash_mult.out matrix=file=ampsdir:md.mat gap_penalty=8.0 constant=8 print_vertical= block_file=bash.bloc,1 seq_file=myoglobins.seq
These commands will mostly be familiar by now!! The only new addition is the block_file command. This defines a block file to be read, the filename must be followed by an integer that identifies the iteration number specified in the block_file. In this example, the iteration number is set to 1.
This block_file contains the alignment described by Bashford et al (1987) for 7 globin sequences aligned on structural grounds. The command file aligns all 60+ myoglobin sequences with this structure based alignment. See file bash_mult.out for the result.