[ssml] Re: Sequence defined domains?

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Thu Nov 27 12:55:14 EST 2003

<quote who="Kevin Karplus">
> I don't know whether Pfam has any HMMs for split domains, but
> Superfamily certainly does, because Julian Gough and I had several discussions
> about the best way to represent them with SAM HMMs.
> It turned out that the usual SAM-T99 or SAM-T2k script does a pretty good job if
> this the inserted domain is put in lower-case and the
> surrounding domain is put in upper-case in the initial seed.

Can I as if using a non split seed can pick up split domains?

I guess I could check this from the superfamily RDB, which looks


> Kevin Karplus
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