1. Average free energy of DNA fragment

The free energy (stability) of a double stranded DNA molecule can be expressed in terms of the free energy of its constituent base paired dinucleotides. Average free energy is determined by the summation of free energy for a sliding window of 15 base pair length over any stretch of DNA sequence.

2. DNA stability

DNA stability is a sequence dependent property and depends on the sum of interaction energy between the constituent nucleotides.

3. E cutoff

Average free energy over known promoter sequences of 100nt length (spanning the region from -80 to +20 with respect to known TSSs).

4. D cutoff

The difference between the average free energy over upstream regions of known promoter sequences (E) and the average free energy over downstream random sequences (REav).

5. True positive (TP)

A predicted promoter region which lies wholly within or atleast partially overlapping with the 200nt region (-150 to +50) spanning a TSS, is considered as a true positive.

6. False positive (FP)

The predicted promoter regions other than true positives are considered as false positives.

7. False negative (FN)

If PromPredict does not locate any low stability signal within a 1000nt long region (-500 to +500) in the vicinity of a known TSS, it is considered as a case of false negative.

8. Potential Promoter

If there is no true positive region identified for a 1001 nts long promoter sequence the nearest false positive in the upstream of TSS is considered as potential promoter.