In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes

Table 3 Summary of RIP mutation in the repeat families of S. nodorum strain SN15.

			RIP Dominance Scores			NCBI NR Protein Blastx			GIRI Repbase Tblastx
Repeat Family	Copy Number	Full Length (bp)	RIP dominance by highest G:C content[20]	RIP dominance by majority consensus	RIP dominance by deRIP consensus	Hits to deRIP consensus	Hits to majority consensus	deRIP Improve-ment factor (Maximum value)	Hits to deRIP consensus	Hits to majority consensus	deRIP Improve-ment factor (Maximum value)
R8	48	9143	2.96	1.95	2.91	126	77	1.96
R10	59	1241	1.91	0.96	2.07	3	2	2.13	0	3
X0	76	3862	2.13	0.97	2.05	1	0		3	1	1.34
R9	72	4108	1.88	0.92	1.77	250	25	2.75	124	4	1.28
Molly	40	1862	1.21	0.64	1.73	250	161	3.78	34	15	1.92
X3	213	9364	0.63	0.81	1.62	11	10	2.8
X35	19	1157	1.5	1.34	1.43	1	0
X96	14	308	0.87	0.89	1.39
X48	22	265	1.82	1.16	1.33
R22	23	678	1.2	0.84	1.28				2	2	1.06
X26	38	4628	1.16	1.08	1.19	57	57	1.38
Pixie	28	1845	0.77	0.57	1.06	250	190	1.79	17	18	1.25
R37	98	1603	0.49	0.25	0.95	0	55		4	18	1.16
R31	23	3031	0.99	0.83	0.9	16	15	1.44	3	7	1.14
X23	29	685	0.45	0.4	0.9				3	3	0.82
X36	10	512	0.89	0.78	0.87	2	1	1.43
Elsa	17	5240	0.86	0.78	0.82	250	231	2.06	65	30	1.44
R51	39	833	0.47	0.31	0.8	0	3		0	3
X11	36	8555	0.83	0.71	0.78	250	250	1.35	250	228	2.18
X12	29	2263	0.67	0.43	0.76	0	1		10	10	1.44
R39	29	2050	0.59	0.28	0.74	173	149	1.54	34	31	1.88
X28	30	1784	0.83	0.59	0.73
R25	23	3320	0.25	0.6	0.65	4	4	1.19	3	1	0.86
X15	37	6231	0.61	0.46	0.61	250	250	1.45	243	217	1.66
R38	25	358	0.2	0.14	0.5

RIP dominance, a measure of the strength of RIP mutation, is reported for all 3 different RIPCAL comparison methods: versus the highest G:C content sequence; versus the alignment 'majority' consensus and; versus the deRIP consensus. Measures of how much the predicted deRIP consensus of a repeat family resembles its original version, hit discovery scores and deRIP improvement factors, are also summarised for comparisons against NCBI NR Proteins via blastx and the GIRI Repbase database of repetitive elements via tblastx.

ISSN: 1471-2164