When the program reads a block_file it generates a lookup table that consists of an array of dimensions (length of the alignment)*(the number of amino acid types). Each element of the lookup table represents the weight assigned to aligning a particular amino acid at that position. MULTALIGN allows you to print out this Table and modify it to increase/decrease the weights for particular amino acids at particular alignment positions. The Table may then be read in by the program and used to subsequently align another amino acid sequence.
Note. This option is meant for application when using MULTALIGN to scan sequence databases with flexible patterns, hence it is only possible to align ONE further sequence with the block_file. (The subject of flexible patterns and database scanning is the basis of a paper shortly to be submitted. The necessary commands to make use of this feature will be added as an appendix once the paper is in print.)
The command 'save_lookup=bash_day.look' causes the lookup table to be written out to the file bash_day.look.
The Table may be modified, then read in by the command 'read_lookup=bash_day.look'
An example command file to generate and save a lookup table is shown below (file 'bash_look.com')
output_file=bash.out matrix=file=ampsdir:md.mat gap_penalty=8.0 constant=8 gap_factor=100 save_lookup=bash_day.look block_file=bash_vg.bloc,1 non_alignment= seq_file=globins.seq
The seq_file command must be present, and at least one sequence present in the seq_file.
The Lookup_table (bash_day.look) might be edited to increase specific residue weights before using it to align another sequence to the block.
An example command file is 'bash_rlook.com'
output_file=bash2.out gap_penalty=8.0 gap_factor=100 read_lookup=bash_day.look block_file=bash_vg.bloc,1 seq_file=myo.seq
This will cause the lookup table to be read and used to score the alignment of the sequence in file myo.seq with the block_file. If more than one sequence is defined in the seq_file then a garbage alignment will be generated for sequences 2-N.