<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 exelent. Cheers, Dan. > Kevin Karplus > _______________________________________________ > ssml-general mailing list > ssml-general at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/ssml-general