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STAMP_CLEAN

This program allows you to tidy up gaps that are not meaningful in the context of a multiple sequence alignment derived from structure. In other words, regions that are not similar across all members of a structural family can be `cleaned' to remove isolated residues aligned in the middle of nowhere. Note that one doesn't always want to do this (since the sub-alignments can be meaningful).

The format is:

    stamp_clean <stamp alignment file> <minimum segment length> > <output file>

The $<$minimum segment length$>$ is the minimum number of residues that is to be considered significant. I always use 3, since this means that short stretches of 1-2 residues that are surround by gaps (i.e. in any sequence) are `cleaned'. Try it and see what I mean.