next up previous contents
Next: Multiple alignment format Up: Input and Output format Previous: Transformations   Contents

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
    Tonin secondary structure  Author's assignments
    ----EEEEE-----EEEEEE-- <etc.> --HHHH---*
    >Kallikrien
    Kallikrien secondary structure -- visual inspection
    ----EEEEEEEE---E-EEEEE--- <etc.> --GGHHHH---*
    >SGprotease
    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.