Table 2a. The numbers of true homologues found in tests 1 and 2, at 1% error rate, for a selected number of methods, concentrating on comparisons of model building and model scoring.

Alignment	Model building and scoring method
	HH	HS	SH	SS
(i)
C-STR	117	113	129	116
G-PFAM	557	590	560	593
G-PFAM-T99-CLW	554	549	560	554
(ii)
1S-BL&CLW	5536	5247	5929	5965
1S-T99-CLW	6620	7205	7559	8128
1S-T99, 1S-T99HAND	7414	7813	8283	8784
(iii)	Number of nrdb90 iterations
	0	3	30
PSI-BLAST	4330	7897	7462

(i) Results for test 1; (ii) for test 2; (iii) results of test 2 applied to PSI-BLAST (the case with zero nrdb90 iterations being pairwise NCBI BLAST). G stands for globins, C for cupredoxins, 1S for a single-sequence seed; PFAM indicates a PFAM alignment, STR a structural alignment, G-1S is the sequence of 1rse; T99 is the SAM T99 procedure, either default (T99), with all columns in the resultant alignment converted to upper case (T99-UC), or realigned with ClustalW (T99-CLW). Finally, HH and SS are the default procedures for HMMER and SAM, respectively, HS indicates a HMMER model converted to the SAM format and scored by SAM, and vice versa for SH. See text for further explanations.