Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

Huson, Daniel H.; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P.; Nieselt, Kay; Williams, Rohan

doi:10.1186/s40168-017-0233-2

Microbiome

Table 1 For each gene family studied, we report the KEGG orthology group, number of reads assigned to that group by DIAMOND, number of reference gene sequences that exist in the synthetic community, and number of reference genes “detected” by each method: MEGAN, IDBA-UD, Ray, SOAPdenovo, and Xander

From: Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

Gene family	KEGG	Reads	References	MEGAN	IDBA-UD	Ray	SOAP	Xander
Acetyl-CoA C-acetyltransferase	K00626	58,135	64	31	16	12	12	23
Archael rpoB1	K03044	17,875	16	7	7	6	3	9
Archael rpoB2	K03045	12,025	16	8	8	6	5	5
Cell division protein	K03531	45,881	48	37	39	12	7	12
Bacterial rpoB	K03043	105,212	64	43	16	12	13	50
Phenylalanyl-tRNA synthetase alpha subunit	K01889	44,779	64	57	56	47	51	48
Phenylalanyl-tRNA synthetase beta subunit	K01890	73,072	64	53	50	42	38	35
Phosphoribosylformylglycinamidine cyclo ligase	K01933	31,919	64	58	59	46	45	54
Ribonuclease HII	K03470	18,707	64	54	55	53	45	48
Ribosomal protein L1	K02863	24,190	64	57	49	45	48	53
Ribosomal protein L10	K02864	23,970	64	58	48	55	57	55
Ribosomal protein L11	K02867	17,113	64	60	50	51	60	59
Ribosomal protein L13	K02871	17,642	64	58	54	53	57	45
Ribosomal protein L14	K02874	13,435	64	56	42	49	58	60
Ribosomal protein L15	K02876	13,087	64	59	56	50	55	55
Ribosomal protein L16	K02878	10,058	64	46	34	36	44	44
Ribosomal protein L18	K02881	14,856	64	57	48	56	57	55
Ribosomal protein L2	K02886	29,849	64	60	54	46	55	57
Ribosomal protein L22	K02890	15,875	64	59	54	55	57	51
Ribosomal protein L24	K02895	11,786	64	60	46	56	58	44
Ribosomal protein L25	K02897	12,941	64	41	41	39	42	41
Ribosomal protein L29	K02904	4913	64	29	8	33	34	8
Ribosomal protein L3	K02906	30,192	64	59	47	51	57	51
Ribosomal protein L4	K02926	14,539	64	44	41	39	43	44
Ribosomal protein L5	K02931	20,533	64	60	58	55	59	58
Ribosomal protein L6	K02933	20,645	64	58	41	56	59	60
Ribosomal protein S10	K02946	11,327	64	56	42	48	56	54
Ribosomal protein S11	K02948	10,793	64	47	43	51	52	56
Ribosomal protein S12	K02950	14,199	64	61	41	48	60	58
Ribosomal protein S13	K02952	13,975	64	59	46	56	60	58
Ribosomal protein S15	K02956	10,795	64	54	16	43	55	50
Ribosomal protein S17	K02961	10,235	64	58	36	49	44	60
Ribosomal protein S19	K02965	12,479	64	59	39	51	59	58
Ribosomal protein S2	K02967	25,926	64	61	46	41	53	48
Ribosomal protein S3	K02982	25,722	64	59	46	48	57	57
Ribosomal protein S5	K02988	21,761	64	59	55	53	53	56
Ribosomal protein S7	K02992	20,520	64	60	42	54	60	61
Ribosomal protein S8	K02994	14,543	64	62	57	58	60	57
Ribosomal protein S9	K02996	12,927	64	59	52	52	58	61
Signal recognition particle protein	K03110	27,386	64	35	48	36	19	46
Two-component system	K03407	47,904	64	29	17	15	15	27
Mean absolute deviation				9.34	19.73	18.24	15.41	14.17

Best results are shown in bold. Mean absolute deviation between the number of references genes and the number detected by each method is reported as a summary statistic

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ISSN: 2049-2618

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