Validation of an NSP-based (negative selection pattern) gene family identification strategy

BMC Bioinformatics

Table 1 dS/dN calculations for phenylalanine ammonia-lyase (PAL) contigs

Comparison		Sd^a	Sn	S	N	ps	pn	ds	dn	ds/dn	ps/pn
Contig1	Contig4	38.50	18.50	62.83	219.17	0.61	0.08	1.27	0.09	14.22	7.26
Contig1	Contig3	42.17	39.83	65.17	216.83	0.65	0.18	1.49	0.21	7.07	3.52
Contig1	Contig9	42.33	36.67	65.50	216.50	0.65	0.17	1.48	0.19	7.73	3.82
Contig1	Contig6	52.50	138.50	63.33	197.67	0.83	0.70	NA	0.00	NA	1.18
Contig1	Contig8	53.50	138.50	63.33	197.67	0.84	0.70	NA	0.00	NA	1.21
Contig1	Contig7	45.17	153.83	62.83	210.17	0.72	0.73	2.39	2.80	0.85	0.98
Contig4	Contig3	211.83	133.17	286.33	985.67	0.74	0.14	3.22	0.15	21.64	5.48
Contig4	Contig9	143.00	105.00	191.67	639.33	0.75	0.16	3.94	0.19	21.27	4.54
Contig4	Contig6	152.50	490.50	201.50	665.50	0.76	0.74	NA	0.00	NA	1.03
Contig4	Contig8	80.33	225.67	99.83	314.17	0.80	0.72	NA	0.00	NA	1.12
Contig4	Contig7	65.00	233.00	93.17	326.83	0.70	0.71	2.00	2.25	0.89	0.98
Contig3	Contig9	1.50	14.50	197.17	633.83	0.01	0.02	0.01	0.02	0.33	0.33
Contig3	Contig6	160.50	486.50	206.83	660.17	0.78	0.74	NA	0.00	NA	1.05
Contig3	Contig8	81.83	222.17	102.83	311.17	0.80	0.71	NA	0.00	NA	1.11
Contig3	Contig7	70.50	228.50	96.00	324.00	0.73	0.71	2.90	2.11	1.37	1.04
Contig9	Contig6	150.00	454.00	196.17	613.83	0.76	0.74	NA	0.00	NA	1.03
Contig9	Contig8	81.33	220.67	103.17	310.83	0.79	0.71	NA	0.00	NA	1.11
Contig9	Contig7	71.67	229.33	96.33	323.67	0.74	0.71	3.61	2.17	1.66	1.05
Contig6	Contig8	2.00	4.00	108.33	305.67	0.02	0.01	0.02	0.01	1.42	1.41
Contig6	Contig7	68.33	200.67	97.50	301.50	0.70	0.67	2.04	1.64	1.25	1.05
Contig8	Contig7	68.33	199.67	97.50	301.50	0.70	0.66	2.04	1.61	1.27	1.06

SNAP output results for all 21 pairwise comparisons of 7 contigs in which an ORF was identified. A ds/dn value greater than 2.00 was chosen as threshold to indicate contigs that potentially represent distinct gene family members.
a – See http://www.hiv.lanl.gov for explanation of abbreviations and calculations.

ISSN: 1471-2105