2 <TITLE> New Features in Version 1.4.5 - Program alsnum</TITLE>
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10 <H1><A NAME=SECTION0009000000000000000> New Features in Version 1.4.5 - Program alsnum</A></H1>
12 Version 1.4.5 includes the program "alsnum". This is a temporary solution to
13 the residue numbering problem. Ultimately, these functions will be included
16 alsnum creates a set of TEXT commands that can be incorporated into an
17 alscript command file to place sequential numbers at any position in the
18 alignment. The numbers ignore gaps, so the numbering will correspond to
19 the specific sequence position rather than the alignment.
23 1. Decide where you want the numbers to be placed. For example, you might
24 want the numbers above the third sequence in the alignment. If so, make
25 an extra sequence space above the third sequence using the ADD_SEQ command.
27 2. Decide what is the number of the first residue of the sequence to be
28 numbered. This will not always be 1 since you may be aligning fragments
31 3. Decide the numbering interval (e.g. every 10th amino acid).
35 For example, if you want to add numbers according to sequence 37 of a
36 block file (junk.blc), calling the first residue of the sequence 12,
37 and with an interval of 5, and the numbers are to be placed at the
38 location of sequence 3 in the alignment. Type:
40 alsnum 37 12 5 3 < junk.blc > junk.text
42 5. Add the resulting TEXT commands from junk.text to your alscript