In order that the output from STAMP may be displayed in a more
attractive manner, a program was developed to translate the
vertical, block-file format of STAMP multiple alignments into input
for GJB's program ALSCRIPT, which can then be used to display the
alignments in Postscript. Details of DSTAMP and how to obtain
ALSCRIPT are given CHAPTER VI. Contact Geoff Barton for a copy of
ALSCRIPT (worth having, even for other sequence alignments).
The program deterimes reliable regions given a set of criteria, and
highlights sequence and secondary structure accordingly.
Another program (VER2HOR) can display STAMP alignments in a horizontal text format for quick viewing (i.e. it takes the vertical format of STAMP output, and changes it to an easy to see horizontal format). This is particularly useful if you don't have ALSCRIPT.
STAMP multiple alignments are always associated with particular superimpositions. It is often useful to show such superimpositions graphically. GSTAMP provides input for Per Kraulis' program MOLSCRIPT. Most structual biology labs have at least one copy of this program, and it is available from Per Kraulis. One simple needs to run TRANSFORM (see below) on a STAMP alignment file, and then run GSTAMP on the same file, followed by separate runs of MOLSCRIPT, to produce separate Postscript files for each aligned structure, with structually equivalent regions shown as ribbons, the rest as trace.