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 a file called:
Which contains a set of ALSCRIPT commands. To get a pretty Postscript alignment, one needs to
The file globin_align.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 boxed in the sequence alignment. Helices and strands will appear as cylinders and arrows (coil/turn regions are not shown). Conserved residues will be in inverse text, positions showing a conservation of polar character will be in bold, those showing conservation of hydrophobic character will be shaded and those showing a conservation of small size will be shown in a smaller font. It is possible to modify the output format (paramaters are described in a Chapter 4). I would also recommend only using the DSTAMP output as a starting point, and refine the ALSCRIPT file yourself to give the best alignment. The automated procedure can give some ugly results.
Figure 1 Globin alignment as discussed in the text.