DSTAMP generates input files for GJBs ALSCRIPT program. Given a STAMP
alignment file, DSTAMP can be run to create a fairly pretty alignment.
Detailed descriptions of the parameters are given below. As a quick
example, using the globin example,
dstamp -f globin.5.clean -prefix globin_align
will create files:
globin_align_als.com globin_align_als.bloc
The first is a set of ALSCRIPT commands and the second is a modified
alignment file. To get a pretty Postscript alignment, one needs to
run alscript:
alscript globin_align_als.com
The file globin_align_als.ps will be created, and is previewable or
printable on a Postscript printer. And is shown in Figure 1.
By default, residues occuring within
structurally equivalent regions will be bold-faced, boxed and in upper-
case, with other regions being lower-case, non-bold and in a smaller
font. All secondary structure assignments will be shown below. It is
possible to modify the output format (paramaters are described in a Chapter 4).
Figure 1 Globin alignment as discussed in the text.