Evaluating deterministic motif significance measures in protein databases

Table 3 Evaluation of contiguous motifs on Prosite data.

PS entry	Motif	NumSeqs	DiffNGrams	Rel. Supp(%)	Supp Rank	ZScore	LogOdd	Pratt	IG	Info
PS00341	IPCCPV	9	702	77.8	9	21	65	166	13	217
PS00415	LRRRLSDS	12	3582	91.6	9	503	1058	2103	11	1784
PS00047	GAKRH	105	653	93.3	21	61	109	216	27	460
PS00984	CFWKYC	19	1256	100	1	1	1	785	1	5
PS00541	SKRKYRK	6	144	100	1	85	110	131	3	134
PS00822	PFDRHDW	9	2251	100	1	1	5	204	1	400
PS00419	CDGPGRGGTC	207	32936	100	1	1	1	3	1	158
PS00349	RKRKYFKKHEKR	18	2929	100	1	38	86	2884	19	310
PS00861	GWTLNSAGYLLGP	32	888	100	1	66	301	179	1	569
PS01024	EFDYLKSLEIEEKIN	60	5527	100	1	620	2427	5266	1	5244
PS00291	AGAAAAGAVVGGLGGY	136	2423	100	1	1033	1770	184	3	1984
R _m					0.2340	4.526E-3	1.854E-3	9.075E-4	0.1358	9.764E-4

Ranking results of eleven Prosite datasets (identified by the Prosite (PS) entry column). For each dataset, the number of protein sequences, the number of different n-grams (Diff NGrams), where n is equal to the motif length and the relative support of the target motifs (Rel. Supp) are presented. Motifs are ranked with Information-theoretic based measures. Ranks obtained by support (Supp Rank) and information gain (Info) are also provided for comparison purposes. Last row gives the R_mvalues of each measure, where best results are obtained by support and IG.

ISSN: 1748-7188