Coverage versus error plots. Coverage versus Error plots for the SSEF, LFF, SGM, and PRIDE2 methods. Given a projection method and a database of protein domains, each query protein domain defines a curve, which plots coverage (the fraction of related protein domains retrieved) against the number of errors (the number of unrelated domains retrieved). To obtain one curve per projection method the individual curves were averaged, first across different queries in the same classification group and then across different classification groups (see Methods). (a) Pairs in the same SCOP family are true positives; pairs in different SCOP families are false positives. (b) Pairs in the same SCOP super-family are true positives; pairs in different SCOP super-families are false positives. (c) Pairs in the same SCOP fold are true positives; pairs in different SCOP folds are false positives. (d) Coverage obtained by projection methods at different classification levels when 300th false positive result is encountered.