Hi, I want to compare protein homology detection quality of my algorithm with psi-blast and delta-blast algorithms. Mainly I'm interested in calculation of Sensitivity, Specificity and ROC Score of psi-blast or delta-blast algorithms like e.g. in the article about delta-blast: Domain enhanced look-up time accelerated BLAST, where there is a comparison between psi-blast, cs-blast, blastp and delta-blast algorithms based on protein remote homology detection.
I have query sequence and resulting database sequences found by psi-blast or delta-blast algorithms ranked by E-Value from lowest to highest. How do I compute True Positive, False Positive, True Negative and False Negative values for my query sequences with respect to protein remote homology detection task. Or simply, how it is computed sensitivity and specificity (and analogously ROC Score) for psi-blast or delta-blast algorithms in the sense of remote protein homology detection.
Thanks for any help.