Table 2.

Number of sequences with correctly identified V, D and J genes or rearrangements in clonally related sequence data sets^a

	IgBLAST	iHMMune-align
Data set 1 (57 sequences)
IGHV4-34*01	52	51
IGHD7-27*01	54	55
IGHJ3*02	52	52
IGHV4-34*01-IGHD7-27*01- IGHJ3*02 rearrangement	47	47
Data set 2 (101 sequences)
IGHV4-34*01	96 (96)b	95
IGHD6-6*01	87 (48)b	86
IGHJ6*02	101 (101)b	97
IGHV4-34*01- IGHD6-6*01- IGHJ6*02 rearrangement	82	80

^aThe clonally related sequences were obtained from Wilson and co-workers (15). Tests were performed using web IgBLAST and stand-alone iHMMune-align (version iHMMune-align_26-11-2007.zip) with default search parameters, except that the mismatch penalty for D gene is set to −1 (instead of default −4) for IgBLAST test with data set 2. The identified germline genes are the top hits (or one of the top equivalent hits that have identical match scores, as well as identical per cent identity) from IgBLAST or iHMMune-align searches. iHMMune-align did not return a D gene match for 1 and 6 sequences for data set 1 and data set 2, respectively. IHMMune-align also did not return any germline gene matches for one sequence in both data sets because of presence of deletions in V gene.

^bResults from IgBLAST using default mismatch penalty for D genes.