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Table 2.

Performance of Aligners on theCFTR Region

	Baboon	Chimpanzee	Mouse	Rat	Cow	Pig	Cat	Dog	Chicken	Zebrafish	Fugu	Overall
Number of exons	232	176	230	230	224	174	176	182	68	48	150	1914
MUMmer
100%	100	99	6	7	28	32	38	28	0	0	0	36
90%–100%	100	100	8	9	40	44	47	37	0	0	0	41
70%–100%	100	100	14	16	52	55	56	45	0	0	0	47
AVID
100%	100	100	94	95	98	97	99	93	66	33	19	88
90%–100%	100	100	98	100	99	100	100	98	79	42	21	91
70%–100%	100	100	100	100	100	100	100	99	85	44	29	92
BlastZ
100%	100	100	97	97	96	97	100	94	96	73	66	94
90%–100%	100	100	100	100	98	100	100	99	97	79	72	97
70%–100%	100	100	100	100	100	100	100	99	97	79	80	98
LAGAN
100%	100	100	97	97	98	97	100	94	96	83	72	95
90%–100%	100	100	100	100	99	100	100	99	99	88	77	98
70%–100%	100	100	100	100	100	100	100	99	100	92	81	98
MLAGAN
100%	100	100	97	97	98	97	100	94	99	88	73	96
90%–100%	100	100	100	100	99	100	100	99	100	98	84	98
70%–100%	100	100	100	100	100	100	100	99	100	100	90	99
Time (sec)
MUMmer	8	6	7	7	8	6	6	6	3	2	2	61
AVID	82	57	215	221	165	111	139	131	83	53	76	1775
BlastZ	31	24	46	43	40	36	34	33	7	5	6	305
LAGAN	56	50	78	82	60	68	62	78	338	158	133	1135
MLAGAN	—	—	—	—	—	—	—	—	—	—	—	4547
Max memory (MB)
MUMmer	40	39	40	40	40	39	39	39	39	38	38	40
AVID	598	551	581	584	578	498	522	502	387	340	360	598
BlastZ	239	276	202	212	204	200	208	206	188	185	185	276
LAGAN	90	90	90	89	90	87	88	87	88	87	89	90
MLAGAN	—	—	—	—	—	—	—	—	—	—	—	670

[i] The annotated human exons were aligned with TBLASTN to createpseudo-annotations of exons in the other organisms. The table reports the percentage of exons covered by alignments over at least 70%, 90%, and 100% of their length, and the time and memory required to obtain the alignments. The last column reports the percentages of exons aligned out of total number of exons, the total time required for the 11 alignments (for the single 12-sequence multiple alignment in the case of MLAGAN), and the maximum memory required.