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Re: STRUCT_REF_SEQ_DIF

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Mon, 11 Mar 96 21:14:13 EST 

Herb Bernstein writes:

> STRUCT_REF_SEQ_DIF could use the token _struct_ref_seq_dif.db_seq_num
> to specify the sequence position at which a point difference occurs
> in terms of the sequence of the referenced database.  While this can
> be inferred by very careful use of _struct_ref_seq.db_align... tokens,
> that is clumsy and error-prone when there are insertions or deletions.

What Herb writes here raises an issue of schema.  When I wrote the STRUCT_REF
data items, my thinking was that the sequence in the data block was intended
to match the referenced sequence in the database in phase - that is, that
we would allow for point differences (ala vs. ile, for instance) but that if
the match involved insertions and deletions, they would have to be handled
via careful use of the alignment beg and end data items.

Now that Herb raises this issue, I realize that we could try and be more
sophisticated about this, but my personal feeling is that this could easily
get out of hand if we tried to do something that would cope with (for 
instance) a 42-residue insertion.  So I am inclined to leave the data itmes
they way they are, but to adjust the definitions for the categories to say
explicitly that insertions and deletions should be handled with appropriate
use of the beg and end of the sequence matched.  But I'll wait for some
comment before I do that.

Paula

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