A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Table 1 # of ORFs annotated by five different domain annotation tools

MG/MT datasets	# Predicted ORFs	Gene3d	Pfam	TIGRFAM	PRINTS&Prosite	MetaCLADE	MetaCLADE +UProC
# of ORFs annotated by each tool
Puerto Rico Rainforest soil metagenome	520 791	189 138	181 777	15 155	27 710	260 953	266 380
Arctic Winter marine ecosystem	358 095	113 307	104 098	6 835	15 324	150 786	158 496
Bone sample from Vindija Neanderthal	74 705	12 793	9 717	612	933	18 589	22 673
Human gut metagenome	45 770	17 873	18 981	905	2 002	27 028	29 645
Human gut metatranscriptome	37 209	10 297	9 699	183	714	16 522	20 479
# of ORFs annotated by one specific tool
Puerto Rico Rainforest soil metagenome	520 791	16 482	1 090	2 473	138	37 811	43 222
Arctic Winter marine ecosystem	358 095	11 564	580	1 703	159	20 531	28 227
Bone sample from Vindija Neanderthal	74 705	1 824	50	294	14	4 663	8 742
Human gut metagenome	45 770	1 368	55	27	7	4 477	7 093
Human gut metatranscriptome	37 209	1 172	20	4	7	3 983	7 938

Number of ORFs (# of ORFs) predicted in reads with FragGeneScan and annotated by different tools. Largest annotations are reported in bold. See Fig. 4 and Additional file 1: Figures S7-S10, S12-S15 for additional information

ISSN: 2049-2618