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Sequence format

When necessary, STAMP programs read sequence information in NBRF (PIR) format. For example, user defined secondary structure assignment might be supplied in a file that looks like:

Tonin secondary structure  Author's assignments
----EEEEE-----EEEEEE-- <etc.> --HHHH---*
Kallikrien secondary structure -- visual inspection
----EEEEEEEE---E-EEEEE--- <etc.> --GGHHHH---*
S. Griseus protease secondary structure.
----EEEEE---EEEE-EEEEEEEE--- <etc.> --GGHGHG---*

This is essentially NBRF (PIR) format. Note the position of the asterix. Comments must be limited to the single line between the >identifier and the start of the sequence string.

Geoff Barton