[ssml] Re: Sequence defined domains?

[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.

Kevin Karplus