Table 1.

Nomenclature of search strategies

Name	Description
HO	Original HMM dataset
HB	HMMs, background insertion emission probabilities
HG	HMMs, constant state transitions and background insertion emissions
PO	PSSMs, converted from original HMMs.
PC	PSSMs, from five PSI-BLAST iterations over nr using profile consensus seeds
PS	PSSMs, from five PSI-BLAST iterations over nr using SCOP domain sequence seeds

As shown in this table, the first two letters of the abbreviations of various search strategies denote the type of profile (HMM or PSSM), and the method of construction. The third letter is optionally appended to show the database of origin (ℱ for Pfam, U for SUPERFAMILY).