hmm on sssdb

I've tried several ways to catagerize the sequences into our motifs.
Dynamic Programming, DTW, FFT, specgram, all failed.
I think it's because they consider everything while we only want it to concentrat on some importent part only.(ex: only strands, not loops, only common part not the gaps)
so, I also tried HMM.
got pretty success using EMBOSS's HMM tools.
ehmmbuild and ehmmpfam