An example command file for this mode is globin_pairs.com. This is shown below:
Commands Explanation number -------- ------------------ output_file=globin_pairs.out 1. mode=pairwise 2. matrix_file=ampsdir:md.mat 3. pairwise_random=100,100,1 4. gap_penalty=8.0 5. constant = 8 6. seq_file=globin.seq 7.
This command file causes all pairwise comparisons to be performed on the sequences in the file 'globin.seq'. In other words, for the 7 sequences sequence 1 is aligned with 2, 1 with 3 and so on. For N sequences there are N*(N-1)/2 comparisons performed.
For each sequence pair (eg. 1 and 2), a full Needleman and Wunch sequence comparison is performed. Then the sequences are shuffled and recompared ( in this case 100 times) in order to find the expected distribution of scores that would be obtained if the sequences were unrelated but have the same length and composition as 1 and 2. Various statistics on the comparisons are then output to the specified output_file (globin_pairs.out).
The output file from this sequence alignment run contains the following information:
A banner describing the program name, source and limitations of use. Information on the maximum length and number of sequences allowed. Information on the commands specified to the program, files etc. A list of the sequences defined in the sequence file. Finally, a set of numerical results of the run in a series of fields as follows.
Field Description ----- ----------- 1 and 2 number describing the sequences aligned on this row. 3 and 4 The lengths of the sequences described in 1 and 2. 5 The match score obtained for the comparison of the two sequences. 6 The number of internal gaps in the alignment (overhangs at the ends are not counted) 7 The number of positions at which two amino acids are aligned. 8 The number of positions at which identical amino acids are aligned 9 Percentage identity (8/7) 10 Normalised Alignment score - The match score divided by the number of aligned positions * 100. (5/7)*100. 11 Alternative Normalised Alignment score - The match score minus the number of gaps times the gap penalty all divided into the number of aligned positions. (7/((5-6)*gap_penalty))*100. 12 Number of randomizations performed 13 mean score for the randomizations 14 standard deviation of the random scores 15 Significance score for the alignment. Given by the mean random score minus the match score all all divided by the standard deviation. (13-5)/14. 16 Comparison number.
This output file is in the correct format for input by the program ORDER. Clearly, however the actual alignments have not been output. If the alignments are required you must include the command line(s)
print_horizontal= (for horizontal format)
print_vertical= (for vertical format)
Note that a file containing alignments cannot be read directly by ORDER. (the alignments would first have to be deleted using a text editor).