WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

BMC Bioinformatics

Table 1 Performance of WeederH on simulated promoter sets

χ²Score Threshold	%pred	Nc	Sc	Sp
0	82.98	94.99	99.21	0.12
1	57.97	88.51	96.45	0.39
2	44.50	85.74	93.30	0.54
3	34.98	82.89	91.73	0.64
5	24.00	78.87	89.37	0.76
7.5	15.59	74.23	85.82	0.85
10	10.90	67.44	77.95	0.90
12	8.33	64.30	73.62	0.93
15	6.15	60.23	69.29	0.95
FP	10.54	61.48	72.44	0.90

Performance of WeederH at different χ² score thresholds on the 254 simulated sequence sets. %pred indicates the percentage of nucleotides of the reference sequence belonging to a motif output by the algorithm. Nc indicates the nucleotide coverage, the percentage of nucleotides in annotated sites matched by a predicted motif (equalling sensitivity); Sc indicates the site coverage, the percentage of annotated sites matched (at least by 75% of their length) by a motif predicted by WeederH; finally, Sp is specificity. The bottom row reports the performance of the Footprinter algorithm on the same set.

ISSN: 1471-2105