HMM
From PhosphataseWiki
The page is under construction.
List of HMMs
PAP_NTD (Purple Acid Phosphatase, N-Terminal Domain)
CDC25_NTD (CDC25, N-Terminal Domain)
General Protocol for HMM building
We usually built the HMMs from PSI-BLAST hits.
To find the domain sequences for building a HMM, we PSI-BLASTed the domain sequence or the full sequence. It sometime matters if you query the region that is supposed to contain the domain (based upon structure or any evidence) or the full sequence. The full sequence is often more sensitive to find weak hits to the domain. We recommended to download the files of Alignment, Search Strategies, and PssmWithParameters of PSI-BLAST result for reproductivity.
