To test the performance of P2TF, a variety of approaches were taken. P2TF data were compared to different analyses available in the literature generated using other search methods. We used these studies as reference sets and calculated sensitivity and specificity to assess the efficiency of the P2TF analysis

Species	Reference TFs	P2TF TFs	Sensitivity (%)	Specificity (%)	Reference
Bacillus subtilis 168	237	281	91.6	98.4	Moreno-Campuzano et al., 2006
Lactobacillus acidophilus NCFM	93	107	93.5	98.9	Wilson et al., 2008
Stenotrophomonas maltophilia R551-3	262	292	93.9	98.8	Wilson et al., 2008
Corynebacterium efficiens YS-314	103	150	97.1	98.3	Brune et al., 2005

Parameters calculation

Sensitivity = TP/TP+FN

Specificity = TN/TN+FP

TP. True positive, TN. True negative, FP. False positive, FN. False negative

References

Brune,I. et al. (2005) The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics, 6, 86.  

Moreno-Campuzano,S. et al. (2006) Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach. BMC Genomics, 7, 147.  

Wilson,D. et al. (2008) DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res, 36, D88-92.