Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions

Siqueira, Gabriel; Alexandrino, Alexsandro Oliveira; Oliveira, Andre Rodrigues; Dias, Zanoni

doi:10.1186/s13015-021-00200-w

Algorithms for Molecular Biology

Table 3 Distances for the IRD problem with and without the use of our partition algorithm

From: Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions

OP	\({\|\Sigma \|}\)	With partition							Without Partition
		Minimum Distance			Average Distance			Time	Minimum Distance			Average Distance			Time
		Min.	Avg.	Max.	Min.	Avg.	Max.		Min.	Avg.	Max.	Min.	Avg.	Max.
25	10	27	33.38	41	30.65	37.20	47.07	5.35	98	100.44	102	105.15	105.84	106.82	14.43
25	20	27	32.64	38	29.44	35.36	41.36	5.11	93	98.04	101	102.56	104.56	105.80	14.21
25	30	28	32.55	38	29.25	34.90	40.69	4.99	88	95.02	99	99.35	102.59	104.50	13.83
25	40	28	32.91	39	28.00	34.65	40.48	4.98	84	92.17	98	95.01	100.47	104.07	13.71
25	50	28	32.62	38	28.00	34.13	39.42	4.96	80	89.46	96	92.96	98.65	102.58	13.26
25	60	27	32.61	39	27.00	33.85	40.81	4.94	78	87.57	98	91.02	97.03	104.22	12.99
25	70	28	32.35	39	28.00	33.64	40.90	4.93	73	85.74	94	87.39	95.04	101.30	12.71
25	80	27	32.69	38	28.04	33.58	39.50	4.97	72	83.86	95	84.09	93.49	101.54	12.40
25	90	27	32.79	38	27.00	33.55	40.39	4.94	72	82.31	92	82.03	91.70	99.34	12.03
25	100	28	32.78	38	28.00	33.48	39.24	4.92	66	81.82	95	80.16	91.52	101.39	12.04
50	10	54	60.94	68	56.67	64.24	71.66	9.38	98	100.83	103	105.48	106.04	106.86	14.48
50	20	52	59.96	68	55.80	63.24	72.77	9.29	97	99.30	101	103.80	105.11	106.16	14.37
50	30	51	59.91	70	53.45	63.03	73.07	9.22	92	97.56	100	101.59	104.05	106.35	14.19
50	40	51	59.86	68	53.22	62.93	71.84	9.28	90	95.72	100	99.79	102.76	104.98	13.93
50	50	50	59.70	67	51.83	62.82	71.34	9.08	89	94.04	100	97.50	101.47	104.42	13.73
50	60	54	59.69	67	55.81	62.55	69.59	9.13	84	92.74	99	93.63	100.16	105.08	13.44
50	70	52	59.48	65	54.02	62.42	69.31	9.02	84	91.46	98	92.73	99.12	103.50	13.34
50	80	51	59.30	68	53.04	62.05	71.22	8.91	83	90.18	97	91.74	97.89	103.89	13.12
50	90	53	59.65	66	55.03	62.23	68.75	9.01	79	89.12	95	89.68	96.90	102.52	12.99
50	100	51	58.68	65	53.30	61.24	68.84	8.96	77	88.71	98	86.47	96.52	102.28	13.00
75	10	67	75.02	81	69.82	78.41	83.89	11.51	99	101.33	103	105.40	106.17	106.67	14.52
75	20	67	75.19	83	70.95	78.60	86.92	11.43	97	99.94	102	104.55	105.55	106.39	14.35
75	30	67	74.70	83	70.08	78.23	86.72	11.56	94	98.79	102	103.79	104.89	106.20	14.33
75	40	68	75.63	82	70.68	79.10	85.96	11.53	93	98.20	101	101.55	104.17	105.73	14.23
75	50	68	74.52	82	70.73	77.93	84.80	11.37	89	96.76	100	99.61	103.13	105.25	14.08
75	60	67	75.07	84	71.77	78.33	88.08	11.44	90	95.81	100	98.14	102.43	105.60	13.87
75	70	63	75.03	85	65.25	78.32	88.19	11.44	86	95.35	100	97.33	101.91	105.08	14.00
75	80	67	74.70	81	69.33	77.70	84.76	11.31	86	94.74	99	95.42	101.16	105.35	13.65
75	90	68	74.97	82	70.67	77.94	85.61	11.50	87	94.00	99	96.41	100.67	106.91	13.73
75	100	65	74.49	82	69.30	77.59	85.82	11.18	84	93.34	100	92.97	99.93	103.94	13.48
100	10	77	83.54	91	80.65	87.27	95.42	13.12	98	101.23	103	105.77	106.25	106.79	14.56
100	20	77	83.34	90	80.43	87.14	93.44	12.89	97	100.65	103	104.04	105.80	106.69	14.45
100	30	75	83.73	91	78.56	87.41	94.77	13.17	97	99.67	102	102.77	105.30	106.59	14.39
100	40	77	83.78	92	79.85	87.43	96.10	12.89	94	98.77	101	100.29	104.46	106.72	14.20
100	50	76	83.76	91	80.52	87.36	95.46	13.02	94	98.42	102	100.86	104.17	106.55	14.25
100	60	77	84.05	91	79.73	87.58	95.06	13.12	93	97.50	101	99.96	103.51	105.93	14.05
100	70	77	84.40	92	79.93	87.91	95.21	12.97	93	97.38	101	99.26	103.16	106.34	14.03
100	80	76	83.95	92	79.82	87.46	95.58	12.95	91	96.94	101	97.99	102.77	105.72	13.91
100	90	77	84.10	93	80.15	87.50	97.68	12.84	93	96.56	101	99.07	102.37	106.41	13.80
100	100	74	84.09	90	76.45	87.45	93.49	13.02	89	96.41	101	96.20	102.10	105.84	13.87

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