AGeNNT: annotation of enzyme families by means of refined neighborhood networks

BMC Bioinformatics

Table 1 Characteristics of InterPro families and resulting SSNs

InterPro family	# seq	Rep-node 100				Rep-node 80
InterPro family	# seq	# nodes	# edges	A-Th	S-Th	# nodes	# edges	A-Th	S-Th
IPR000312	21,626	17,712	71,376,439	190	107	5446	6,789,466	195	97
IPR004651	10,868	8521	36,297,962	140	101	1830	1,672,923	104	88
IPR023016	9463	7428	27,581,256	144	78	1920	1,842,066	114	67
IPR015890	29,878	14,614	96,362,962	259	96	8388	31,307,224	259	86
IPR007115	10,421	7848	12,511,920	70	40	2901	1,609,102	57	34

The first column gives the name of the InterPro family and the second one the number of sequences belonging to this dataset. The four columns entitled Rep-node 100 and Rep-node 80, respectively, list the number of nodes and edges of the corresponding SSN and the thresholds A-Th and S-Th. For the generation of the dataset, the BLAST E-value cut-off 1E-5 was used

ISSN: 1471-2105